Assessment Endpoints

Assessment endpoints are environmental characteristics of a water body that represent the desired environmental condition described by the management goals. They also are valued ecosystem characteristics that are worth protecting. An assessment endpoint can be a measurable indicator of a biological community (e.g., seagrass, benthic communities) or a physical or chemical characteristic within the water body (e.g., turbidity, dissolved oxygen [DO]). Because assessment endpoints can be measured, they provide a useful indicator that can link nutrient pollution to management goals (e.g., what nutrient concentration would allow the designated use such as fisheries or recreation to be maintained?). Water quality managers can use this linkage between nutrient concentrations and the assessment endpoints to identify concentrations of nutrients that would support designated uses. 

Assessment endpoints can be measured directly or indirectly:

Endpoint Examples of Measures
Seagrass Acreage, density, species composition, historic depth of colonization
Phytoplankton Chlorophyll a concentrations, species composition, microscopic counting, biovolume estimation (e.g., ash-free dry weight)
DO Direct measure of dissolved oxygen (e.g., using DO meters)
Clarity Secchi depth, turbidity, light attenuation (e.g., photosynthetically active radiation)
“Assessment endpoints are explicit expressions of the actual environmental value that is to be protected, operationally defined by an ecological entity and its attributes” (Guidelines for Ecological Risk Assessment, USEPA 1998). 

More Information:

  • Management goals
  • Aquatic life uses
  • Human health uses
  • Aquatic life relevance
  • Human health relevance
  • Illustrating sensitivity to nutrients
  • What is important to stakeholders

Assessment endpoints should have the following characteristics:

    • Relevance to protecting and maintaining the ecological conditions of a water body or class of waters
    • “Ecologically relevant endpoints often help sustain the natural structure, function, and biodiversity of an ecosystem or its components.”
    • Sensitivity to nutrient inputs
      • What is the effect on the endpoint of change in nutrients?
      • How quickly does the endpoint respond to nutrient changes?
    • Relevance to protecting management goals for a water body or class of waters
      • Does the endpoint reflect ecological values that are important to the public?
      • Can the endpoint be used to address the water body’s regulatory requirements?
    • Measurable
      • Can the ecological entity/characteristic and its attribute be measured directly or indirectly?
    • Availability of data
      • Are there sufficient data available to conduct analyses (i.e., sufficient in both quantity and quality)?

Examples of assessment endpoints include the following:

    • Phytoplankton biomass
    • Seagrass health
    • DO
    • Benthic communities
    • Water clarity

After deciding whether an ecosystem entity/characteristic is appropriate to use as an assessment endpoint for nutrient criteria development and how to measure it, water quality managers can use the information obtained to identify a numeric target value that represents attainment of the designated use.

Identifying Potential Assessment Endpoints

hen you are trying to identify potential assessment endpoints, a good first step is to look at the management goals for a water body with respect to nutrients and develop a general list of biological, physical, and chemical factors representative of the desired ecological condition. The choices of assessment endpoint will be narrowed down based on the type of water body and existing regulatory management goals.  For instance, if protection of aquatic life is a management goal, an assessment endpoint might include some measure of the biological community in the water body or a desired concentration of DO that would be needed to protect that goal.

To determine which ecological entity or characteristics could make effective and useful assessment endpoints for the nutrient criteria you wish to derive, ask the following questions:

How relevant is this potential endpoint to the management goal and designated use?
  • Are there any statutory requirements stipulating what is to be protected (e.g., specified DO criteria; acres of seagrass)?
  • Does the endpoint represent an ecological outcome, condition, process, or activity that scientists, the public, and water quality managers want to protect? Examples include:
    • Endangered species or ecosystems
    • Commercially, recreationally, or culturally important species
    • Aesthetic values such as swimmable beaches
Is the potential endpoint ecologically relevant?
  • Is the potential endpoint an important part of its ecosystem? Is it functionally related to other features in the ecosystem? If so, to what degree?
  • What are the effects of nutrients on the potential endpoint and to what degree are they expressed (e.g., when an increase in nutrients causes a dramatic negative change in the attribute of value)?
  • What are the spatial and temporal scales of the effects of nutrients?
  • What is the potential for recovery from nutrient impacts?
  • What level of ecological organization is adversely affected by nutrient pollution?
Is the potential endpoint sensitive to nutrient pollution?
  • Is there a demonstrable relationship between nutrients and the potential endpoint? If so, what is that relationship?
  • Is the potential endpoint directly affected by nutrients or by nutrient-related impacts?
    • Often, impacts further down the effects pathway can take longer to manifest and also be influenced by other confounding stressors.
    • Are there other stressors or natural disturbances that might confound, lessen, or exacerbate the effect of nutrients on the potential endpoint?
What is the level of exposure of the potential endpoint to nutrients?
  • What are the typical magnitudes, durations, and frequencies of exposure to nutrients?
    • What concentration of nutrients supports the endpoint?
    • At what concentration of nutrients would one expect to see adverse impacts?
What is the fate and transport history of the potential endpoint and nutrients in the system?
  • How and where do nutrients enter and move through the water body? What is the residence time?
    • Does the potential endpoint express nutrient effects at the same time it was exposed or a different time? In the same place it was exposed or a different place?
    • Nutrients are usually not conservative, which leads to different concentrations in different parts of a water body. As a result, responses to nutrients can be site-specific depending upon the amounts transported.
  • For a biological endpoint, nutrient sensitivity can be influenced by individual or community life history characteristics
    • Species with short life cycles and high reproductive rates can express the effects of nutrients quickly.
    • Is there a life stage of the potential endpoint that is particularly sensitive to nutrients? Often early stages of aquatic life are more sensitive than later stages, but different life stages can be affected (e.g., larval, nesting, migrating, breeding, molting).

Indications that your endpoint is sensitive

  • Change in primary productivity as nutrients increase
  • Increase in respiration rate with nutrient pollution
  • Changes in primary producer community structure due to increases in nutrients (changes in abundance and richness)
  • Changes in aerial coverage
  • Changes in concentration

Ways to measure assessment endpoint sensitivity

  • Chlorophyll a (primary productivity)
  • DO (respiration rate)
  • Species percent (changes in plant community structure)

What factors affect sensitivity

  • Fate/transport and retention of nutrients
  • Presence of other stressors or natural disturbances
  • Residence time
  • Response time lags

Selecting an Assessment Endpoint Representative of the Management Goal

There are two elements that you should identify when you are defining an assessment endpoint:

  • The specific attribute or entity representative of the ecological condition the criteria aim to protect
  • The characteristic of that attribute or entity that responds to nutrients and is important to protect

For a biological endpoint, an attribute or entity could be an individual species, a community, a functional group (e.g., primary producers), an ecosystem, or a particular habitat (e.g., seagrass). For a chemical or physical endpoint, the attribute could be a specific concentration or level that is measureable. Sometimes, you already have identified an attribute when you were selecting potential endpoints; but at other times, an ecosystem characteristic might need a little more specificity. For example, on one hand, you might have already identified seagrass as being important. But, on the other hand, your goal might be to protect aquatic system health, in which case, you need to define what entities are representative of good system health.

Next, consider characteristic of the assessment endpoint responds to nutrient inputs and should be protected or maintained. It could be the count, density, concentration, coverage, biomass, community composition, survival, growth, or some other aspect that is impacted by nutrients and is important to protect.

Some guidelines to keep in mind when selecting assessment endpoints:

  • Unlike management goals, assessment endpoints are neutral and do not express any statement as to their desired state.
  • As with management goals, your assessment endpoint must be as clear and as specific as possible. For example, concepts like health, integrity, and unimpacted are vague and should be clearly defined. Selecting organisms or concentrations that are considered representative of these terms can be helpful.

Selecting Assessment Endpoints for Numeric Nutrient Criteria Derivation—Data Needs

To ensure that an assessment endpoint is suitable for numeric nutrient criteria (NNC) derivation, the relationship of the selected entity or attribute to nutrients should be well-documented in the available literature. Additional factors to consider when selecting an attribute or entity as an assessment endpoint include:

  • Data availability—Because data are key to criteria derivation analyses, it is important to consider the data requirements for describing the endpoints and make statistical inferences about the relationships between the assessment endpoint and nutrient levels of impairment.
    • What are the available data types, locations, temporal and spatial coverages, quality, and quantity?
    • What are the data needs for the potential types of analysis? For example, stressor-response relationships can be data-intensive and will require enough data for the type and number of parameters being investigated.
    • Data limitations and uncertainty should be acknowledged.
  • Spatial and temporal representativeness—The available data should provide information about the ecological expectations for the selected endpoint within the water body of concern over time, including the presence and absence of an endpoint within the water body, in a specific location, during a certain season, and throughout the year.
    • Do the data represent the times and places pertinent to criteria development?
    • Do the data show when and where the response to nutrients occurs?

Quantifying the Level of Protection after Criteria are Established

Assessment endpoints not only are used to qualitatively connect the management goal to the water quality-related attributes requiring protection. They also are used to establish the numeric threshold for nutrient enrichment within the water body of concern. Setting the numeric threshold is done in two steps. First, identify a measurable effect of nutrients on the assessment endpoint. This measure of effect often is established when defining the assessment endpoint. For example, you might have selected seagrass aerial coverage as the assessment endpoint. In that case, the measure of effect is the aerial coverage of seagrass. In other instances, you might need to be more specific in describing exactly what about the assessment endpoint you want to measure. For example, your assessment endpoint might be macroinvertebrate community composition. In this case, you need to define exactly what you want to measure as the metrics of community composition (e.g., an Ephemeroptera, Plecoptera and Trichoptera (EPT) richness, percent model affinity, richness, or functional feeding groups). Another example could be setting your assessment endpoint as DO to maintain healthy aquatic life in a water body. In that case, you need to know what concentration of DO would be necessary to keep specific species of fish or benthic communities alive.

The next step in the process is to set numeric targets, or water quality targets, for the measures of effect. The water quality targets are used in developing nutrient criteria to quantitatively define the level of nutrients that represents the ecological condition expressed by the management goal. The quantitative target can be used to statistically determine whether the water body is supporting the valued components of the ecosystem, and thus the management goals. In this case, it would be the basis for deriving nutrient criteria values.

To determine a protective water quality target value, consider what level of the assessment endpoint is representative of the management goal for the system. You can accomplish this by reviewing pertinent contemporary and historical literature. Research done of the system of interest can provide direct insight into the behavior of the local ecosystem. That data might not be available, however, in which case literature collected in similar systems can be informative. In addition to literature, input from experts familiar with the system or similar systems can help guide your decision. You then can synthesize the sources to decide on what level of the endpoint indicates support of the management goals for the system. A helpful tool that has been used successfully in a variety of settings is a decision-making framework, which you can use to guide the process. Regardless of the method you use, it is important to document all of the choices you made and resources you used to set the water quality target.

Note: In instances in which measureable data are not available to support the selection of an endpoint, you cannot use that endpoint for numeric criteria derivation. Additionally, each endpoint you select to represent the management goal should have a numeric water quality target supported by the literature-available information. If data do not support a water quality target related to nutrients, the endpoint cannot be used to support numeric criteria derivation.

Using the available data, we have compiled a list of potential assessment endpoints for each water body type that meet the criteria described in this section. Each example includes an assessment endpoint, a description of the valued attribute or entity, the measure of effect, and the water quality targets that can be used in statistical analysis. The endpoints presented are viable options to consider when initiating the process of the NNC derivation. You are not limited to the examples provided.

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Description: Phytoplankton are free floating, photosynthetic microscopic organisms. It is important to remember that some phytoplankton species are adapted to freshwater environments, while others live in more saline waters.

  • Relevancy to management goals:

    As a key food source, phytoplankton are vital to supporting aquatic life. However, unbalanced phytoplankton populations can be detrimental to aquatic life and human health uses.

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    Phytoplankton – Relevancy to management goals (more info): In a healthy ecosystem, phytoplankton provide the base of the food web, but when nutrients fuel excessive volumes of phytoplankton, ecological imbalance results. Nutrient-driven algal growth and biomass accumulation can result in more frequent, intense, and lasting blooms of one or more algal species. Fauna that feed on phytoplankton will initially benefit from increased food sources; however, as the system becomes hypoxic and phytoplankton begin to die, higher trophic levels will suffer. These events can decrease water clarity and adversely affect aesthetics, aquatic life, commercial fishing, and recreation (e.g., fishing, swimming, and boating). They also can manifest as harmful algae, which can produce toxins that adversely affect both aquatic life and human health through exposure to airborne/waterborne toxins or consumption of shellfish contaminated with algal toxins.
  • Ability to measure:

    Phytoplankton can be measured by microscopic counting, electronic particle counting, and determination of chlorophyll a concentration.

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    Phytoplankton – Ability to measure (more info): The two basic attributes of phytoplankton most often sampled are biomass and composition. Biomass is the mass of phytoplankton in the water column (i.e., the amount present), and composition is the taxonomic makeup of the phytoplankton assemblage (e.g., the diversity of species present).

    Biomass is typically measured using extraction and analysis of photopigments with a variety of methods, the most common being the spectrophotometric or fluorescence analysis of chlorophyll a. Water column chlorophyll a often is used as a proxy and a particularly common metric for phytoplankton biomass as well as an indirect measure of primary production. Photopigment-based analysis is an estimate of biomass only, as photopigment composition varies across different algal taxa and even within taxa across a variety of environmental conditions. Biovolume estimation based on microscopy or cytometry and imaging is another approach to estimating biomass.

    Composition is primarily measured using collection and microscopic identification to the lowest practical taxonomic level, and other methods are evolving as gene-based techniques improve. The composition of phytoplankton is generally described by size class, species, or taxonomic composition. Size class is nominally defined as microplankton (20-200 micrometers [µm]), nanoplankton (2-20 µm), and picoplankton (< 2 µm).

  • Ecological relevance:

    Long-term elevated concentrations of phytoplankton can adversely affect habitat quality and aquatic life. They shade light from submerged aquatic vegetation (SAV) and decrease dissolved oxygen (DO) through their respiration and decomposition.

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    Phytoplankton – Ecological relevance (more info): Phytoplankton dominate primary productivity in many types of water bodies, accounting for roughly half of the oxygen produced by all plant life on the planet and providing carbon that is the basis for the majority of oceanic, estuarine, and terrestrial aquatic food webs (Thurman 1997). Photosynthetic microalgae form the base of many food chains and thus are the primary producers of the organic matter and energy for higher trophic levels in aquatic habitats. The higher phytoplankton concentration and the shift in phytoplankton composition might change the dissolved oxygen level and alter trophic structure through adverse effects on larvae and fisheries species.

  • Data needs:

    Biomass data are routinely monitored, and data are generally abundant for most water bodies. Satellite-derived data often are readily available for estuarine and coastal waters.

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    Phytoplankton – Data needs (more info): Biomass data in water bodies are routinely collected, and data are generally abundant. In coastal, estuarine, lake, and reservoir waters, phytoplankton also can be assessed via remote sensing of chlorophyll a. Remote sensing platforms (e.g., satellites, aircraft) are capable of detecting optical components such as chlorophyll a and their respective concentrations in the water column according to the wavelengths of light they individually reflect back to the sensor.

  • Sensitivity to nutrients:

    Phytoplankton have fast growth rates and respond rapidly to increases in nutrients. Nutrient pollution can cause increases in the maximum and mean concentrations of phytoplankton.

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     Phytoplankton – Sensitivity to nutrients (more info): Phytoplankton have fast growth rates and rapidly respond to nutrient inputs over a wide range of concentrations and intensities.

  • Public importance:

    Unusually high concentrations of phytoplankton, known as blooms, can adversely affect aesthetics, recreation, and aquatic life habitat. Harmful algal blooms also can affect human and aquatic health by producing a variety of toxins.

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    Phytoplankton – Public importance (more info): Impacts of phytoplankton concentration and composition shifts include fish kills and alterations of aquatic trophic structure through adverse effects on larvae and other life history states of commercial and recreational fisheries species. Other potential effects include fish kills, human intoxication or even death from contaminated shellfish and fish, and death of marine mammals and seabirds.

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Description: Macroalgae, also referred to as “seaweed,” are macroscopic and multicellular algae that generally grow on relatively shallow, rocky substrata. They typically belong to one of several groups of multicellular algae, including red algae, green algae, and brown algae. Unlike seagrass, macroalgae have no roots, stems, leaves, or vascular tissues.

  • Relevancy to management goals:

    Macroalgae are important primary producers in some coastal regions and provide a food source for the higher trophic organisms.

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    Macroalgae – Relevancy to management goals (more info): Despite the beneficial role of macroalgae in balanced systems, macroalgal blooms in eutrophic systems are unaesthetic, problematic to aquatic life, and potentially detrimental to the ecosystem.
  • Ability to measure:

    Species richness and species diversity, the two most basic attributes measured for macroalgae, are sampled through aerial photography, remote sensing, and field survey. Aerial density can also be used to quantify macroalgal populations.

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    Macroalgae – Ability to measure (more info): Macroalgae taxonomy can be challenging because identifying them is often based not only on simple morphological criteria, but also on reproductive structures and types of life history, cross-sectional anatomical details, types of growth, and cytological and ultrastructural criteria. 
  • Ecological relevance:

    Macroalgae serve as a nutrient filter in ecosystems. Blooms develop, however, when sufficient nutrients are present, resulting in low levels of dissolved oxygen, high turbidity, and disruption of phytoplankton, submerged aquatic vegetation, coral reefs, and higher trophic levels.

  • Data needs:

    Data are needed from field surveys or aerial photographs.

  • Sensitivity to nutrients:

    While macroalgae do not respond as rapidly to environmental changes as phytoplankton, they have been widely noted as an important response to nutrient pollution.

  • Public importance:

    Macroalgae have a variety of usages, including as food sources and chemical ingredients.

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    Macroalgae – Public importance (more info): In addition to providing a food source and a chemical ingredient, macroalgae also provide essential habitat for a variety of important commercial and recreational species. Macroalgal blooms, however, can be problematic to ecosystems and disruptive to designated uses such as drinking water, recreation, and aesthetics.

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Harmful Algal Blooms (HABs)

Description: Harmful algal blooms (HABs) are excessive growths and accumulations of algae that create health hazards for humans or animals through the production of toxins and/or as a result of their high biomass levels. They also can degrade aesthetic, ecological, or recreational values.

  • Relevancy to management goals:

    Phytoplankton are critical for maintaining the health and balance of aquatic life; however, HABs negatively impact other organisms by reducing water clarity and creating hypoxic conditions. They also impair drinking water and recreational uses through the production of toxins and excessive biomass levels.

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    HABs – Relevancy to management goals (more info): HABs can impact many uses of water bodies. Blooms that produce toxins negatively impact recreational uses because of the health problems that might occur if people or animals ingest the toxins. They also cause taste and odor problems in drinking water sources and reduce aesthetic values. Aquatic life also is negatively impacted by high biomass blooms that cause low-oxygen events as well as block light penetration into the water column. In addition, some HABs such as golden algae blooms are toxic to fish. 
  • Ability to measure:

    The intensity of HABs can be characterized or measured in a variety of ways, including Secchi disk depth, chlorophyll a concentration, cell identification and count, analysis of microcystin and other cyanotoxin concentration, and satellite imagery.

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    HABs – Ability to measure (more info): HAB species can be identified through microscope and gene-based techniques. They are characterized or measured in a variety of ways, including Secchi disk depth, chlorophyll a concentration, cell counts, analysis of microcystin and other cyanotoxin concentration, and satellite imagery. Measurements of HABs and HAB-generated toxins also are being measured by sensors in the field using hand-held units or autonomous platforms.  
  • Ecological relevance:

    Algae play a critical role in aquatic ecosystems as primary producers and the base of the food chain; however, when excessive levels of nutrients trigger bloom conditions—especially of the cyanobacteria algal group—the overgrowth disrupts the food web, reduces light penetration into the water column, and often creates low-oxygen conditions that harm other species.

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    HABs – Ecological relevance (more info): HABs can damage ecosystems by preventing light from penetrating the water column, as well as creating hypoxic conditions when they respire and decompose. Blooms also disrupt the food web; alter community structures of fish, benthic fauna, and other aquatic life; and emit toxins harmful to other organisms.

  • Data needs:

    Site-specific, long term empirical data of cyanotoxins, chlorophyll a, and other measures of algal bloom characteristic are needed.

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    HABs – Data needs (more info): Site-specific, long-term empirical data of cyanotoxins, chlorophyll a, and other measures of HAB characteristics are needed to support documenting, detecting, and predicting blooms. The challenge in measuring HABs is their spatial and temporal unpredictability and relatively short life span. 

  • Sensitivity to nutrients:

    HABs are generally associated with increases of nutrient loading and overenrichment of aquatic ecosystems.

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    HABs – Sensitivity to nutrients (more info): Nutrient-overenrichment is one of the primary causes of HABs. Cultural and hydrologic modifications that increase nutrient loading, affect flushing rates, modify the food web (e.g., by reducing grazing zooplankton), and other factors also can trigger HABs. 

  • Public importance:

    The primary concern with HABs is their potential toxicity to animals and people as well as their increased biomass, which impairs drinking water, recreation, fishing, and other beneficial uses.

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    HABs – Public importance (more info): The primary concerns with HABs is their potential toxicity to animals and people as well as their increased biomass, which impairs drinking water, recreation, fishing, aesthetics, and other beneficial uses. HABs also impact shellfish, which accumulate toxins as they filter water, making them toxic for human consumption. 

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Diatom Assemblages

Description: Diatoms are a major group of algae that include species ranging from very sensitive—or intolerant—to very tolerant of disturbances to their natural habitat.

  • Relevancy to management goals:

    A natural balanced diatom community helps support aquatic life in the ecosystem by functioning as a primary producer and as a food source for higher organisms.

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    Diatom assemblages – Relevancy to management goals (more info): Healthy, balanced diatom communities help support aquatic life in an ecosystem by functioning as primary producers and as food sources for higher organisms. A healthy community structure, in terms of composition, diversity, and functional organization, is indicative of stream reaches that are maintaining the high level of biological integrity required to support a healthy balance and diversity of aquatic life. 
  • Ability to measure:

    Stream diatom assemblages are characterized by identifying and enumerating diatom species in the community and classifying them based on taxa sensitivity.

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    Diatom assemblages – Ability to measure (more info): The Biological Condition Gradient (BCG) characterizes stream diatom assemblages by categorizing sites by level of impairment based on nutrient concentrations and other factors. Using the BCG enables streams to be categorized based on their biological conditions and scientifically defensible nutrient criteria to be established to protect the biotic integrity of streams in each category. Once BCG categories are determined, stream diatom assemblages can be categorized based on taxa sensitivity. As a result, when a sample is analyzed for diatoms, the number of taxa in each sensitivity group can be determined and the resulting assemblage can be placed in the appropriate biological condition category. 
  • Ecological relevance:

    Healthy and diverse diatom communities are an important part of the food web, serving as primary producers and as food for zooplankton, macroinvertebrates, and other higher organisms.

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    Diatom assemblages – Ecological relevance (more info): Some species of diatoms are more sensitive to—or less tolerant of—changes to their natural environment than others. Natural, pristine stream reaches that support a balanced set of native taxa, including sensitive diatom species, are able to maintain their structural and functional integrity within a range of natural variability. Increasing levels of human disturbance that change biological conditions in a stream usually trigger shifts within diatom communities to more species with higher tolerance levels and fewer sensitive species. This shift is a general indication of reduced biological integrity of the system as a whole. 

  • Data needs:

    Site-specific collections of diatom species within defined resource community boundaries.

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    Diatom assemblages – Data needs (more info): Once the BCG classification system is developed, the diatom species in a site-specific sample are identified, enumerated, and, based on the number of taxa in each sensitivity, assemblages are determined and grouped into sensitivity categories.

  • Sensitivity to nutrients:

    The assemblage of taxa within a diatom community is determined by nutrient levels and other factors that define biological integrity. Increases in nutrient levels trigger shifts in community structure toward more tolerant species.

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    Diatom assemblages – Sensitivity to nutrients (more info): Nutrient levels are one of several factors that affect diatom assemblages as well as the overall biological integrity of a stream reach. Streams with larger populations of highly sensitive taxa are associated with lower nutrient levels while more highly tolerant taxa are found in streams with higher nutrient levels. 

  • Public importance:

    Natural stream systems supporting healthy diatom assemblages also tend to support desirable native fisheries that increase recreational values and opportunities.

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    Diatom assemblages – Public importance (more info): Natural stream systems supporting healthy diatom assemblages, including sensitive diatom taxa, also tend to support desirable native fisheries and other healthy aquatic life, which also tends to increase recreational values and opportunities. 

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Water Clarity

Description: Water clarity is a measure of how far light penetrates into the water column; the deeper light penetrates, the clearer the water.

  • Relevancy to management goals:

    Many forms of aquatic life such as seagrasses depend on water clarity levels that allow light to penetrate the water column and reach the bottom.

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    Water clarity – Relevancy to management goals (more info): Adequate amounts of light penetrating the water column are critical for maintaining healthy photosynthetic communities, including SAV, corals, and desirable macroalgaes (e.g., kelp communities) which, in turn, are crucial for supporting diverse healthy benthic and fish ecosystems. Good water clarity also increases the quality of recreational uses such as fishing, swimming, and aesthetic values. 
  • Ability to measure:

    Water clarity is most often measured in lentic (still) waters using a Secchi disk, while total suspended solids (TSS) and turbidity measurements are used to characterize water clarity in lotic (flowing) waters.

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    Water clarity – Ability to measure (more info): Water clarity is most often measured in lentic (still) waters using a Secchi disk, while TSS, color, and turbidity measurements are used to characterize water clarity in lotic (flowing) waters. Secchi disk measurements are made in situ by lowering a disk until it just disappears from view. Turbidity and color measurements are made either in situ or in the laboratory using an optical sensor. TSS are analyzed in the laboratory by drying a sample and weighing the amount of material left. 
  • Ecological relevance:

    Aquatic primary producers, including algae and submerged aquatic vegetation (SAV), require adequate amounts of light to photosynthesize and create energy and oxygen essential for fueling a healthy ecosystem.

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    Water clarity – Ecological relevance (more info): Water clarity dictates the amount and depth of light that can penetrate into the water column and, therefore, controls primary production (e.g., the depth and extent of SAV and phytoplankton). Primary producers are the base of the food web and play a critical role in the transfer of energy and nutrients throughout the aquatic ecosystem. SAV also traps and stabilizes sediment, helps reduce nutrients in the water column, and provides shelter, habitat, and feeding and spawning areas for fish, benthic fauna, and other organisms. Reductions in water clarity are usually the result of unbalanced increases in phytoplankton and/or suspended sediment particles and can harm SAV and benthic organisms because of decreased light penetration and increased sedimentation. 

  • Data needs:

    Site-specific, long-term, Secchi disk depth data are needed for lentic waters, and suspended solids and turbidity data are needed for lotic waters.

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     Water clarity – Data needs (more info): Site-specific, long term empirical data are needed to establish historical and baseline data for water clarity. These data can be Secchi disk, turbidity, color, and/or TSS measurements.

  • Sensitivity to nutrients:

    Increases in nutrient pollution can trigger increased growth of phytoplankton in the water column that reduce water clarity.

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    Water clarity – Sensitivity to nutrients (more info): Increases in nutrient pollution can trigger increased growth of phytoplankton in the water column, which reduces water clarity and restricts light penetration in the water column. This situation can reduce the diversity and productivity of aquatic life the system can support. 

  • Public importance:

    Good water clarity promotes healthy ecosystems and enhances recreational activities such as swimming and fishing.

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    Water clarity – Public importance (more info): Water clarity is important for maintaining aquatic habitat for sport fishing and shellfish populations as well as for providing more pleasing waters for recreational uses such as fishing, swimming, and aesthetic values

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Benthic Faunal Communities

Description: Benthic faunal communities are the collection of organisms that inhabit the bottom substrates of water bodies and include species that range from very sensitive (intolerant) to very tolerant of disturbances to their natural habitat.

  • Relevancy to management goals:

    Benthic faunal communities are important for supporting aquatic life, especially as food sources for fish and other aquatic animals.

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     Benthic faunal communities – Relevancy to management goals (more info): Communities in freshwater environments are primarily made up of insect larvae, mollusks, and worms. Marine environments are usually dominated by annelids, mollusks, and crustaceans. They support aquatic life uses because of their key role within the food web, serving as a food source for fish and other organisms and breaking down organic matter.
  • Ability to measure:

    Benthic faunal communities are characterized by identifying and enumerating species and classifying them based on function and sensitivity (tolerance) to disturbances.

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     Benthic faunal communities – Ability to measure (more info): The health of benthic faunal communities is traditionally measured using a multimetric index that basically reduces complex information about community form and structure into a simple numerical value. The index is usually based on measures of key community attributes such as species diversity and composition, the presence of pollution-tolerant and pollution-sensitive species, and feeding habits. New indices are being developed that focus specifically on assemblages that are sensitive to nutrient levels.
  • Ecological relevance:

    Benthic organisms are an essential part of the food web, feeding on and breaking down organic matter as well as serving as food for fish and other organisms.

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     Benthic faunal communities – Ecological relevance (more info): Benthic species are very diverse and fill many functional roles in the ecosystem that support the balance and natural flow of energy and nutrients. Some feed on algae and bacteria, and others shred and eat leaves and other organic matter. They also are important food sources for fish and other higher organisms. A healthy benthic faunal community generally indicates a water body with a high degree of biological integrity. Individual species, however, display varying levels of tolerance to changes in water chemistry and physical habitat. Such disturbances can trigger shifts in community structure by decreasing the number of pollution-sensitive species and increasing the number of pollution-tolerant species. This sensitivity arises from the close relationship between benthic organisms and sediments, their relative immobility, and their relatively long life cycles, all of which results in the ability to accumulate environmental contaminants over time. Shifts in the structure of benthic faunal communities can negatively impact the food web and disrupt the structure and viability of aquatic life throughout the system.

  • Data needs:

    Site-specific collections of benthic faunal communities are needed from defined areas.

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     Benthic faunal communities – Data needs (more info): Once an index is developed, site-specific, long-term, species-level data on nutrient-sensitive benthic faunal community attributes and associated nutrient water quality data are needed to generate an index value that characterizes the health of the benthic faunal community.

  • Sensitivity to nutrients:

    The assemblage of taxa in the benthic faunal community is determined by nutrient levels as well as other factors that define biological integrity.

    More Info

     Benthic faunal communities – Sensitivity to nutrients (more info): Benthic fauna as a group are generally not considered directly sensitive to nutrient levels, but symptoms of cultural eutrophication, including increased primary production, can profoundly change water chemistry and physical habitat and impact the benthic faunal community structure to the point of destroying it if anoxic conditions develop. In general, when human disturbance occurs, sensitive species of benthic fauna are replaced by species that are more tolerant of changing conditions.

  • Public importance:

    Stream systems supporting healthy benthic faunal communities also support native fisheries and provide recreational opportunities.

    More Info

     Benthic faunal communities – Public importance (more info): Natural aquatic systems supporting a healthy benthic faunal community that includes sensitive taxa also tend to support desirable native fisheries and other healthy aquatic life, which also tends to increase recreational values and opportunities.

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Description: Epiphytes are naturally occurring primary producers that attach to surfaces of plants or other objects and often are called attached algae.

  • Relevancy to management goals:

    Increase in epiphyte biomass, growth, and density could affect submerged aquatic vegetation (SAV) growth through light attenuation, thereby affecting aquatic life use.

  • Ability to measure:

    Epiphytic biomass is typically quantified as chlorophyll a using various methods, including ash-free dry weight and biovolume of algae. Composition of the assemblage is quantified through direct sampling and taxonomic identification to species or lowest practical taxonomic resolution.

  • Ecological relevance:

    Epiphytic algal assemblages provide energy to grazers and to the food web.

  • Data needs:

    Species composition is difficult to measure, and epiphyte biomass and density are not usually monitored.

  • Sensitivity to nutrients:

    Epiphytes are known to be highly sensitive to nutrient inputs. They can respond with an increase in biomass, growth rates, densities, and species composition.

    More Info

     Epiphytes – Sensitivity to nutrients (more info): An increase in nutrient inputs can cause a cascading effect. An increase in epiphytes caused by increased nutrients can encrust leaf surfaces of SAV, reducing available light to the plant leaves and affecting the health and survival of the SAV.

  • Public importance:

    Epiphytes can affect the health of SAV. SAV are valued by the public because of the role they play in sustaining valuable resources (e.g., fisheries, wildlife, and water clarity).

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Description: Corals are marine invertebrates that include soft and hard corals. Coral reefs occur in clear, shallow waters throughout tropical regions. Reefs are formed from calcium carbonate skeletons, built by tiny coral animals that make up large coral colonies.

  • Relevancy to management goals:

    The health of corals can affect commercial uses and recreational uses that include swimming, fishing, and boating.


  • Ability to measure:

    There does not appear to be a standardized method to measure coral health or growth.


  • Ecological relevance:

    Corals are highly productive systems and provide habitat and nursery areas for many aquatic species.

    More Info

     Coral – Ecological relevance (more info): Coral reef communities are the most diverse communities on Earth, often described as the rainforests of the sea. Coral reefs provide important habitat and nursery grounds for fish and invertebrates as well as protection from wave and storm damage.

  • Data needs:

    Corals are not regularly monitored and would need to be monitored.


  • Sensitivity to nutrients:

    The response of corals to nutrient inputs can be direct or indirect. Corals require light to survive. An increase in nutrients can cause an increase in primary production. Increased turbidity resulting from the higher level of primary production could block the sunlight corals need.

    More Info

     Coral – Sensitivity to nutrients (more info): Coral reefs are biologically diverse ecosystems well known to be sensitive to low-level nutrient concentration increases, and their response to those impacts can be direct or indirect. Corals thrive in clear, nutrient-poor water, relying primarily on energy derived from photosynthesis by their zooxanthellae, symbiotic algae that live in coral tissues. Zooxanthellae require light to function, so shading from plankton is detrimental to the coral reef function (Salm 1983). Small increases in nutrient input are capable of producing deleterious effects in sensitive coral reef communities (Bell 1991; Lapointe et al. 1997). Chlorophyll a is the most sensitive indicator of eutrophication on coral reefs (Laws and Redalje 1979). While not as clear as chlorophyll a, inorganic phosphorus also is considered a sensitive indicator of nutrient enrichment, while dissolved inorganic nitrogen (DIN) is considered a less sensitive indicator (Bell 1992; Laws and Redalje 1979).

  • Public importance:

    Corals provide important aesthetic value. Reefs provide habitat for fish and other aquatic species.


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Dissolved Oxygen

Description: Dissolved oxygen (DO) is a measure of how much oxygen is dissolved in water and potentially available to aquatic organisms for respiration.

  • Relevancy to management goals:

    The health of aquatic and biological communities depends on sufficient DO in the water column; in other words, low DO and eutrophication directly affect designated uses such as aquatic life use and commercial and recreational fisheries.

  • Ability to measure:

    DO has well-established and practical means of measurement, including using a DO meter and the iodometric method.

    More Info

    DO – Ability to measure (more info):

    The two principal methods for measuring DO are a DO meter and the iodometric (or Winkler) method.

    DO meters often are used to continuously measure DO levels as part of real-time water quality monitoring programs. Real-time monitoring captures short- and long-term changes in water quality, including diurnal and seasonal trends in DO concentrations. Membrane sensors are deployed in the field, and data are logged on-site. When configured with telemetry, data can be transmitted in real-time from a remote site to a project computer or website. DO meters, whether used for single measurements or to continuously monitor DO, often are paired with temperature, pH, and conductivity measurements. Fouling is a concern for deployed probes.

    The iodometric—or Winklermethod is a titrimetric procedure based on the oxidizing property of DO. The iodometric test fixes the DO using reagents to form an acid compound that is then titrated. The point at which the color changes is equivalent to the amount of oxygen dissolved in the sample.

  • Ecological relevance:

    Low DO (i.e., anoxia or hypoxia) impacts aquatic life, with effects ranging from mortality to chronic impairment of growth and reproduction.

  • Data needs:

    DO data are routinely monitored, and data are generally abundant.

  • Sensitivity to nutrients:

    A decrease in DO is a secondary symptom of an increase in nutrient inputs—increased respiration from an increase in primary producers and increased decomposition of organic material by microbial stimulation.

    More Info

     DO – Sensitivity to nutrients (more info): A decrease in DO is a secondary symptom of an increase in nutrient inputs: increased nutrients cause increased respiration from an increase in primary producers and increased decomposition of organic material by microbial stimulation. 

  • Public importance:

    Low DO could trigger fish kills and mortality of benthic communities such as shellfish.

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Submerged Aquatic Vegetation (SAV)

Description: Submerged aquatic vegetation (SAV) are rooted, underwater plants that occur widely in fresh and salt waters. In estuarine and coastal waters, SAV are often referred to as seagrasses.

  • Relevancy to management goals:

    SAV provides food and shelter for fish and wildlife, thereby supporting aquatic life uses.

    More Info

    SAV – Relevancy to management goals (read more): SAV is often considered a “foundation” species in aquatic systems, providing physical substrates to support growth and reproduction of a variety of species; supporting complex food webs; and providing habitat and food for many fish, birds, invertebrates (and endangered species such as manatees and green turtles, where applicable), thereby supporting aquatic life uses. In addition, SAV provides unique and aesthetic submerged vegetated landscapes that support shellfishing, tourism, recreation, and education.
  • Ability to measure:

    SAV is measured by coverage, density, species composition, and historic depth of colonization.

    More Info

    SAV – Ability to measure (read more): Changes in seagrass health in response to nutrient-caused stress are commonly measured through the use of aerial photography or surveys to measure alterations in area, density, biomass, growth rate, and productivity.
  • Ecological relevance:

    SAV trap and stabilize sediments, help reduce nutrients in the water column, and provide important shelter, habitat, feeding, and spawning areas for many juvenile and adult aquatic species.

    More Info

    SAV – Ecological relevance (read more): In addition to providing habitat and food for fish, birds, invertebrates, and endangered species such as manatees and green turtles (where they exist), SAV fulfills a variety of ecosystem functions. Some examples are coastal protection, erosion control, and water purification. SAV attenuates waves, provides sediment stabilization and soil retention in the vegetation and root structure, and provides nutrient and pollution uptake, retention, and particle deposition.

  • Data needs:

    Site-specific long term empirical data on coverage, density, species composition, and historic depth of colonization and associated water quality (especially water clarity) is needed.

    More Info

    SAV – Data needs (read more): Site-specific long-term data sets are needed to establish historical and baseline data for SAV. Aerial distribution (coverage), biomass, taxonomic composition, and historic depth colonization and associated water quality data are important to fully understand SAV trends and ideal water quality conditions to maintain healthy SAV habitat.

  • Sensitivity to nutrients:

    Nutrient pollution negatively impacts SAV by causing increased growth of macroalgae and phytoplankton, which in turn decreases the amount of light available for photosynthesis.

    More Info

    SAV – Sensitivity to nutrients (read more): Changes in SAV distribution or widespread loss often indicates changes in environmental characteristics, including light attenuation promoted by nutrients (via phytoplankton, epiphytes, macroalgae, turbidity). Other environmental factors may also play a role, such as temperature, turbidity, hydrodynamic factors, current and wave exposure, sediment, physical disruptions, bioturbation, disease, and herbivory. Nutrient impacts on SAV are generally indirect. An increase in nutrients in the water column can lead to an increase in primary production (i.e., phytoplankton, macroalgae, and epiphytes) which prevents light from reaching SAV, affecting its growth and survival. The mechanism of nutrient impacts on SAV are well-understood, however, because it is an indirect response, the response time can be slow.

  • Public importance:

    SAV are valued by the public because of the role that they play in sustaining valuable resources (e.g., fisheries, wildlife, water clarity).

Case Studies

Salmon Habitat Indicators

  • 15 salmon habitat indicators to evaluate Northwest streams
  • 5 categories: fish abundance, water quantity and quality, land use/land cover, physical habitat

Ontario Phosphorus Criteria

  • Proposed an plan to allow a 50% increase in P above predevelopment levels
  • Two primary trophic status indicators were selected based on recreational and aquatic life use
  • Water clarity chosen based on its relationship to aesthetic changes in water quality
  • DO chosen as an indicator of production of lake trout

Yaquina Estuary, OR

  • Macroalgal biomass and seagrass examined as practical indicators of cultural eutrophication
  • Eelgrass habitat (measured by water clarity) determined to be a viable endpoint

Remote Sensing in FL

  • Phytoplankton biomass in Florida waters was identified as the endpoint
  • Phytoplankton biomass was measured as satellite-based chlorophyll a

Pensacola Bay

  • Healthy benthic communities as measured by DO in bottom waters
  • Healthy SAV communities as measured by areal extent of colonization

Coastal Bays in MD and VA

  • HABs (e.g., brown tide blooms) occur annually with increasing intensity
  • Macroalgae are abundant and increasing in some areas
  • Hypoxia occurs in many locations
  • SAV is affected by turbidity

Barnegat Bay-Little Egg Harbor

  • Healthy SAV communities as measured by areal extent of colonization
  • Healthy shellfish populations that support sustained shellfishing activities

Yaquina Estuary

  • Looked at chlorophyll a, DO, turbidity, phytoplankton blooms/species composition, and seagrasses

San Francisco Bay

  • Suspended solids increase turbidity and light availability, limiting phytoplankton and SAV growth
  • Spring diatom blooms routinely occur
  • Hypoxic events do not occur regularly

Nutrients in Neuse River Estuary

  • Algal blooms occur at various times of the year
  • Water clarity is affected by CDOM, suspended sediment, and algal biomass
  • Stratification major cause of bottom water hypoxia

Nutrients in Chesapeake Bay

  • Benthic communities affected by hypoxia
  • SAV growth affected by decline in water clarity caused by sediment and algal blooms
  • Algal bloom events occur from increased nutrient inputs

Nutrients in Delaware Estuary

  • Blooms consistently occur in spring when the estuary stratifies, in the mid-estuary
  • Chlorophyll a higher in tidewater river
  • Turbid upper bay area
  • Low DO occurs in the urban river region, but usually not a problem
  • SAV and macroalgae do not exist

Nutrients in Narragansett Bay

  • Several assessment endpoints were examined in this case study
  • Endpoints included phytoplankton, algal blooms, macroalgae, DO, benthic communities, and clarity

North Bosque River Nutrient Targets

  • Phosphorus was identified as the limiting nutrient
  • Established relationships between in-stream phosphorus and chlorophyll a concentrations

Lake Waco Restoration Targets

  • Soluble reactive phosphorus was identified as the limiting nutrient in the lake
  • Established a significant linear relationship between soluble reactive phosphorus and in-lake algal biomass

NH Estuaries Project: Shellfish

  • 12 shellfish indicators to monitor oyster and clam health
  • Indicators include a variety of measures to quantify overall health

NH Estuaries Project: Env. Indicators

  • Indicators: eelgrass, juvenile finfish, fish returns, and lobster and wintering waterfowl abundance
  • Restoration goals measured in acreage of habitat types

San Francisco Estuary Indicators

  • Suite of indicators development from key concepts in the literature
  • 12 primary indicators each consisting of several indices/metrics (total of 47 metrics)

Ecological Indicators

  • Suite of indicators using key concepts from the literature
  • Indicators grouped by management categories
  • Indicators developed by habitat type within  management category

San Francisco Bay Endpoints

  • Primary indicators—DO, phytoplankton, cyanobacteria, and macroalgae
  • Supporting indicators—HAB and toxin concentration, urea and NH4, light attenuation, epiphyte load

Assessment Framework for SF Bay

  • Primary indicators—DO, phytoplankton, cyanobacteria, and macroalgae
  • Supporting indicators—HAB cell counts and toxin concentration, urea and ammonium, light attenuation, and epiphyte load

Nutrient Effects in CA Streams

  • The CA NNE framework proposes to establish regulatory endpoints for algal abundance, DO, and pH
  • Found adverse effects of nutrients on benthic chlorophyll a, AFDM, BMI and algal community structure

Recommended Criteria for WV Lakes

  • TP criterion that will ensure DO is sufficient in the epilimnion
  • Chlorophyll a criteria proposed by the Virginia Academic Advisory Committee

Proposed Criteria for Tampa Bay

  • Areal extent of seagrass was chosen as the assessment endpoint
  • Adopted a goal of reaching 95% of the areal extent of SAV found in the 1950s

Tidal James River Chl-a Criteria

  • Healthy and balanced phytoplankton communities
  • River segment- and season-specific algal levels as measured by chlorophyll a concentration

SAV Targets in MD and VA Coastal Bays

  • NPS has focused on SAV habitat as an indicator of water quality health
  • NPS has looked at chlorophyll a, TSS, light attenuation, DIN, and DIP

Nitrogen Thresholds, MA Embayments

  • Identified several habitat indicators of primary concern
  • Focused on eelgrass, macroalgae, benthic communities, and DO

Eutrophication in Waquoit Bay, MA

  • Increased nitrogen inputs have led to increased phytoplankton blooms
  • Eutrophic conditions have led to a decrease in SAV, increase in macroalgae, and decreased DO

Seagrass Recovery in Tampa Bay

  • Increased phytoplankton biomass and loss of water clarity resulted in SAV loss
  • SAV chosen as the assessment endpoint

Low DO in Skidaway River

  • Increased nutrient inputs are causing increases in phytoplankton production and bacteria
  • Hypoxia can occur directly from microbial

Low DO in Hood Canal, WA

  • Hypoxia and fish kills are associated with eutrophication
  • An increase in phytoplankton and primary production is considered a major cause of hypoxia

Texas Brown Tide

  • A combination of factors caused the bay system to transition to a brown tide-dominated system
  • Auteoumbra lagunensis brown tide caused a shift in the ecosystem

Chl-a in San Francisco Bay

  • Suspended sediment was the limiting factor for primary production in the ’70s and ’80s
  • Watershed projects decreased sediment inputs, which increased water clarity
  • Increased water clarity increased phytoplankton biomass

Nutrient Trends in MD Coastal Bays

  • Submerged aquatic vegetation serves as an indicator of water quality health in Maryland Coastal Bays
  • Nutrients, chlorophyll a, and SAV abundance of has shown degrading conditions in the bays

Nutrients Threaten Coral Reefs

  • Increased nitrogen inputs have affected the coral reef habitat
  • Symptoms are phytoplankton blooms, macroalgae, turf algae, and decreased water clarity

Casco Bay Water Quality Index

  • Developed the Casco Bay Water Quality Index using DO and water clarity
  • Red tide outbreaks were considered as an indicator of anthropogenic eutrophication

Nutrient TMDL for Klamath River, OR

  • Periphyton was determined as the endpoint
  • Established relationships between DO and pH targets and planktonic algal growth and nutrients
  • Recommended setting response targets for benthic algal biomass based on maximum density

Chesapeake Bay Criteria

  • Selected endpoints are DO, water clarity, and chlorophyll a
  • Endpoints are associated with specific habitats during specific time periods
  • DO and water clarity are numeric criteria; chlorophyll a is a narrative criterion

Bow River, Alberta

  • Algae, macrophytes, and periphyton were indicators of periphytic biomass
  • Reduced nutrients led to decrease in Cladophora and other filamentous algae
  • N reduction was associated with decline in macrophytes
  • P reduction decreased periphyton biomass

Nutrients During Low-flow Conditions

  • Examined impacts of nutrients on algae, periphyton, and water clarity
  • Found that abundance and composition of phytoplankton are better indicators of trophic conditions

Nutrient TMDL in the Rockies

  • Developed a 10-year plan to reduce algae concentrations to meet designated uses
  • Target chlorophyll a concentrations were developed based on in situ chlorophyll a data and literature reviews
  • Target values were developed for the growing season

Florida Everglades Phosphorus

  • Looked at periphyton, macrophytes, benthic communities, DO fluxes, and loss of habitat
  • DO provided an important indicator of shifts in aquatic metabolism

Lake Champlain TP Criteria

  • User surveys were used to monitor clarity, algae, odors, fish kills, and overall aesthetics
  • User surveys were paired with chlorophyll a, TP, and Secchi depth to find quantitative relationships

Defining Natural Conditions

  • Algal productivity (measured as chlorophyll a) was used as an assessment endpoint
  • Identified conditions based on algal blooms, water clarity, DO, and blue-green algae
  • Trophic conditions also were used as an assessment index

Wisconsin Lake Phosphorus Criteria

  • Looked at water clarity and chlorophyll a
  • Developed a TSI that showed associations between water clarity, chl-a, and TP

Nutrient-Enriched Waters Designation

  • Determined that a planktonic measure would be easiest to sample
  • Chose phytoplankton as the endpoint

Estuarine Criteria in Florida

  • Seagrass health, balanced phytoplankton biomass, and faunal communities
  • Other endpoints considered include macroalgae, coral, water clarity, fish, and benthic communities
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