Biological monitoring, or biomonitoring, is the use of biological responses to assess changes in the environment, generally changes due to anthropogenic causes. Biomonitoring programs may be qualitative, semi-quantitative, or quantitative. Biomonitoring is a valuable assessment tool that is receiving increased use in water quality monitoring programs of all types.

There are two types of biomonitoring. One type of biomonitoring is surveillance before and after a project is complete or before and after a toxic substance enters the water. The other type of biomonitoring is to ensure compliance with regulations or guidelines or to ensure water quality is maintained.

Biomonitoring involves the use of indicators, indicator species or indicator communities. Generally benthic macroinvertebrates, fish, and/or algae are used. Certain aquatic plants have also been used as indicator species for pollutants including nutrient enrichment (Phillips and Rainbow, 1993; Batiuk et al., 1992). There are advantages and disadvantages to each. Macroinvertebrates are most frequently used (Rosenberg and Resh, 1993). Biochemical, genetic, morphological, and physiological changes in certain organisms have been noted as being related to particular environmental stressors and can be used as indicators.

The presence or absence of the indicator or of an indicator species or indicator community reflects environmental conditions. Absence of a species is not as meaningful as it might seem as there may be reasons, other than pollution, that result in its absence (e.g., predation, competition, or geographic barriers which prevented it from ever being at the site) (Johnson et al., 1993). Absence of multiple species of different orders with similar tolerance levels that were present previously at the same site is more indicative of pollution than absence of a single species. It is clearly necessary to know which species should be found at the site or in the system.

Sentinel organisms

Sentinel organisms, or indicator species that accumulate pollutants in their tissues from the surrounding environment or from food, are important biomonitoring devices (Phillips and Rainbow 1993; Kennish 1992). The Mussel Watch is one such use of a sentinel species (Phillips and Rainbow 1993; Kennish 1992). Filter feeders, such as bivalves (clams and mussels), tend to concentrate metals in their gills or other tissues. The widespread blue mussel (Mytilus edulis) accumulates metals in certain tissues over time. As a result, M. edulis became a species monitored in U.S. waters as well as internationally for changes in levels of pollution (Phillips and Rainbow 1993; Kennish 1992). Seaweeds, (e.g., Fucus spp.) accumulate metals. Older algal tissue can be compared to newer tissue in the same individual to determine the history of contaminants in an area (Phillips and Rainbow, 1993). Metals and organochlorines accumulate in finfish and territorial species or non-migratory species such as pike, largemouth bass, can be used for an accurate indication of mercury and organochlorine pollution in a water body (Phillips and Rainbow, 1993).

Extreme Uptake

Barnacles Zinc   (Zn)
Bivalve mollusks   Copper (Cu), iron (Fe), manganese
Gastropod mollusks    Cu, Zn
Isopods, amphipods   Cu, Fe, Pb, Zn
Polychaetes    Cu


Moderate Uptake

Macroalgae (seaweeds)    Most metals
Mussels/other bivalves    Metals, metallothioneins
Polychaetes    Cadmium (Cd), Pb
Decapods (crayfish)    Cd, Pb
Finfish    Cd, Pb

(Adapted from Phillips and Rainbow, 1993)


Assessment Methodology

When the pollutant type is known or well understood, certain indicators are more effectively used or are less expensive. When stressors are not known and/or less is known about species tolerance levels, multiple level assessment and more intensive and expensive studies that may include toxicity tests may be necessary (Johnson et al., 1993). Multiple level assessment involves the monitoring of indicators and behavioral changes of organisms. Indicators must display a biochemical, genetic, morphological, or physiological change. Behavioral indices are determined by particular species, populations dynamics, or community changes.

Community level biomonitoring provides information on the magnitude and ecological effects of the stressor on the system. Cause and effect relationships are difficult to establish and few definitely exist, because possible confounding factors are often present (Johnson et al., 1993). Using indicators at different organizational levels (for example, individuals, species, community, ecosystem) may be more reliable.

Biomonitoring measures may be used at the different, but related, levels of analysis:

Levels of Organization and Associated Biomonitoring Measures

Individual - Organism - genetic mutations - reproductive success - physiology - metabolism - oxygen consumption, photosynthesis rate - enzyme/protein activation/inhibition - hormones - growth and development - disease resistance - tissue/organ damage - bioaccumulation Population - survival/mortality - sex ratio - abundance/biomass - behavior (migration) - predation rates - population decline/increase Community - Abundance ("evenness") of an organism or organisms - Biomass - Density of an organism or organisms - Richness (variety) - number of species, size classes, or other functional groups, per unit area or volume, or per number of individuals. - Diversity - the richness given the relative abundance of each species or group. Ecosystem - Mass balance of nutrients (from Adamus and Brandt, 1990)

Assessment Indices

There are various indices used to assess the effects of stressors on (aquatic) populations and communities:

Biotic Indices: generally specific to the type of pollution or the geographical area; they are used to classify the degree of pollution by determining the tolerance of an indicator organism to a pollutant. Indicator species are assigned scores for their tolerance level. Biotic indices assume that polluted sites or systems will contain fewer species than unimpacted sites or systems and the species that are present will reflect their particular sensitivity to a pollutant (Johnson et al., 1993). The measures are generally weighted and may include indices such as richness, pollution tolerance, trophic levels present, abundance, and deformities (Adamus and Brandt, 1990). These indices were originally devised for, and are most useful for, organic pollution (Johnson et al., 1993).

Diversity Indices: the measure of the richness, or number of distinct taxa (e.g., orders, families, species) at a site, and the evenness, the relative abundance of different taxonomic groups, determined by counts of all organisms collected.

Comparison, or Similarity Indices - the comparison of the community structure in richness and/or evenness over time or over space.

Both the diversity index and the similarity index may use the functional feeding group (e.g. herbivores, detrivores, carnivores) as a measure of the community integrity rather than taxa (i.e. species, genus, family).

On the level of the individual or species, biochemical and physiological indicators may be examined (Johnson et al., 1993). Some benthic macroinvertebrates such as stoneflies (plecoptera), caddisflies (trichoptera), mayflies (ephemeroptera), and shellfish, show increases or decreases of certain enzymes, changes in DNA, RNA, amino acids, and protein production, oxygen consumption and ion concentration, in response to environmental stressors such as temperature shifts, metals, and pesticides. Physiological indicators of contamination include deformities, sores, or lesions (Phillips and Rainbow, 1993; Kennish 1992).

The EPA Rapid Bioassessment Protocol for Use in Streams and Rivers (Plafkin et al., 1989) uses community diversity in assessing water quality. The absence of pollution sensitive benthic macroinvertebrate groups (ephemeroptera, plecoptera, and trichoptera) and dominance of pollution-tolerant groups (oligochaetes or chironomids), is indicative of pollution. Overall, low richness of benthic macroinvertebrates may indicate impairment. However, naturally low nutrient levels in pristine headwaters may be the cause of low productivity and few benthic macroinvertebrate species exist in these conditions.

Pollutant stressors tend to cause slime and filamentous algae productivity and/or fewer fish species and more tolerant species than expected (Plafkin et al., 1989). The judgment of impairment, based on these indicators should be made by an experienced biologist.

Common Organisms used for Biomonitoring

Benthic macroinvertebrates Advantages: Disadvantages: (Sources: Plafkin et al.,1989; Rosenberg and Resh, 1993; Klemm et al., 1990) Example invertebrate indicators of specific impairment types: Nutrient enrichment - increased ratio of aquatic worms (oligochaetes) to aquatic insects - increased ratio of midges (chironomids) to other aquatic insects - increase of herbivorous mayflies (ephemeropterans) and midges Low dissolved oxygen - increased ratio of aquatic worms to aquatic insects - increased ratio of midges to other aquatic insects Contamination by heavy metals - increased ratio of aquatic worms to aquatic insects - increased ratio of midges to other aquatic insects - increased abundance of water bugs and water beetles - increased ratio of predators to herbivores and detrivores Sedimentation - decrease in mayflies and midges Low pH - loss of snails, clams, mussels, daphnids, mayflies, midges Temperature - Releases of heated effluents tend to reduce community richness (source: Adamus and Brandt, 1990)

Finfish Advantages:

(Plafkin et al. 1989)


Certain fish species such as salmon, trout, perch and sculpins, are less tolerant of pollution than others. Bottom dwellers are more tolerant of organic pollution since they are adapted to lower oxygen levels. Predatory species that use sight to hunt, such as pike, are sensitive to turbid conditions (De Lange 1994).


Extensive fish kills are indicative of severe oxygen depletion caused by organic pollution, oil slicks, or severe toxic pollution, including toxic bacteria or plankton. Erratic behavior, such as swimming close to the surface, slow movements, swimming in circles, and gasping for oxygen, are indicative of water contamination or severe oxygen depletion (De Lange 1994).


Example indicator fish species by impairment type:

Oxygen depletion Darter species Salmonids Sculpin species Benthic insectivores Sedimentation Darter species Salmonids Sculpin species Benthic insectivores Degradation of pools and vegetative cover Sunfish species (Centrarchids) Minnow species (Cyprinids) Salmonids Physical and chemical degradation of the water resource (long lived species) Suckers (Catostomids) Adult trout Minnows Catfish Tolerant species - distinguish low from moderately degraded waters Green sunfish Common carp White sucker Bullhead Creek chub Dace Trophic level Tolerance (overall) used for the Index of Biotic Integrity Omnivores Carp tolerant White sucker tolerant Bullhead minnow intermediate Fathead minnow tolerant yearlings Insectivores Insectivorous cyprinids intolerant to intermediate Juvenile trout intolerant Cutthroat trout intolerant Rainbow trout intolerant Brook trout intermediate White crappie intermediate Paiute Sculpin intolerant Torrent Sculpin intolerant Prickly Sculpin intermediate Reticulate Sculpin tolerant Madtom intolerant Carnivores Salmon intermediate Bass intermediate Pike intermediate Walleye intermediate Yellow perch intermediate Lake trout intermediate (source: Plafkin et al., 1989)


Algal growth is dependent on sunlight and nutrient concentrations. An abundance of algae is indicative of nutrient pollution (De Lange 1994)

Algae are sensitive to some pollutants at levels which may not visibly affect other organisms in the short term or may affect other communities at higher concentrations.


(Plafkin et al., 1989)

Biomonitoring "Rapid Assessment" Measures for Macroinvertebrates and Fish

Measure 1. Number of macroinvertebrate taxa (e.g. family, genus) at site Reason for Use of Measure Taxa richness tends to decline as water quality declines Issues Difficulty in identification results in underestimatation. Richness measures counts at the level of the order or family may ignore the range of pollution tolerance across the family, genus, or even species level. Measure 2. Number of EPT benthic macroinvertebrate taxa (ephemoptera, plecoptera, and trichoptera) to species level if possible Reason for Use of Measure These orders tend to be sensitive to pollutants Issues Species level keys only available for 1/2 of taxa. Presence/absence of taxa is a measure as well. Part of Plafkin et al., 1989. Measure 3. Number of aquatic worms, midges, and/or snails Reason for Use of Measure: Abundance of such groups indicates nutrient enrichment, low dissolved oxygen, and heavy metal contamination. Issues Measure is most useful if you can see a change over time. Measure 4. Niche Occupant Forms Counts are of number of forms, not individuals Reason for Use of Measure Number of niche occupant forms declines as water quality declines Issues: Based on taxa that a novice biologist can discern. Faster. May count different life stage of same taxon as different taxa and therefore overcount. Measure 5. Number of native fish species; benthic species (sucker species); darter species; pool species (sunfish species); long-lived species; tolerant species; intolerant species Reason for Use of Measure: Determines level of degradation Issues: Knowledge of water body composition prior to pollutant makes measure most accurate. Introduction or stocking of species may cause a misrepresentation of actual stream integrity.

Evenness (Abundance) Measures

Measure 1. Number of individuals Reason for Use of Measure Pollutants may cause numbers or biomass to increase (for example, nutrients) or decrease (for example, pesticide). Issues: Competition and predation cause population changes as well. Simple counts of individuals will miss more subtle indications of stress such as physical condition or physiological changes. Used by Plafkin et al., 1989. Measure 2. Ratio of ephemoptera, plecoptera, and trichoptera (EPT) (benthic macroinvertebrate) species to chironomids (midges) Reason for Use of Measure: Chironomids (midges) are considered more pollution-tolerant. In particular, chironomids respond to nutrient enrichment and eutrophic conditions (Adamus and Brandt, 1990). EPT taxa are more sensitive to heavy metals. Issues At the species level of chironimids, a range of pollution tolerances exists. Habitat can influence abundance. Mean size of kick screen must be small enough to ensure chironimids are captured. Measure 3. Ratio of individuals in numerically dominant taxa to total number of individuals Reason for Use of Measure: Domination by few species or families indicates stress or conditions which preferentially support particular taxa such as nutrient enrichment, low dissolved oxygen, and toxic contaminants. Issues Unstressed habitats may have few taxa. Measure 4. Proportion of tolerant fish species of total number collected Reason for Use of Measure: Domination by few species or families indicates stress or conditions which preferentially support particular taxa such as nutrient enrichment, low dissolved oxygen, and toxic contaminants. Measure 5. Proportion of fish with disease/deformities, etc. Reason for Use of Measure: High levels of toxic compounds may generate physical abnormalities.

Functional Feeding Group Measures

Measure 1. Ratio of shredders to total. Collect samples from leaves or other coarse particulate organic matter (CPOM). Reason for Use of Measure: Shredders and their microbial food are sensitive to toxic substances and habitat modification. Issues Identifications must be accurate. Counting the same taxon of a different age group is a problem. Seasonality influences data; easily processed litter such as maples and birch generally have high shredder content in the winter; whereas oak, beech, pine litter have high shredder content in the summer (Plafkin et al., 1989). Measure 2. Ratio of scrapers to collector feeders Reason for Use of Measure These groups indicate availability of food resources. Collector-feeder dominance indicates organic enrichment. Decline of filtering collectors is indicative of toxic contaminants, as toxicants bind to their food particles. Issues Some scrapers are pollution-tolerant. If toxic compounds are present in the organic matter, this measure may not be clearcut. Identifications must be accurate. Measure 3. Ratio of specialists to generalists. Reasons for Use of Measure Specialists are restricted to specific food sources; generalists use a broader range of food sources. Issues Assumes that generalists are more pollution-tolerant and become numerically dominant. Difficult to identify whether and organism is definitely one or the other. Measure 4. Proportion omnivorous, insectivores, carnivorous fish Reason for Use of Measure Assumes there would be more omnivorous fish as environment deteriorates; as the invertebrate community is reduced, insectivores decrease; top carnivores will bioaccumulate pollutants so their presence is indicative of high integrity. Issues Score habitat using Plafkin et al. (1989) system. (Adapted from Resh and Jackson, 1993; Plafkin et al., 1989; Adamus and Brandt, 1990)

Sampling Techniques

Collection of a representative sample and accounting for inherent high variability is a much larger issue for biomonitoring than it is for physical or chemical monitoring.

Benthic Macroinvertebrates

Sampling Techniques- Finfish

Sample as soon as water temperatures are favorable.

Sampling time considerations include migration, spawning, and dispersal. Nighttime sampling is suggested, particularly for catfish and perch.

Some sources of information and techniques for biomonitoring:

Web pages:


Batiuk, R.A., R.J. Orth, K.A. Moore, W.C. Dennison, J. C. Stevenson, L.W. Staver, V. Carter, N.B. Rybicki, R.E. Hickman, S. Kollar, S. Bieber, P. Heasly. 1992. Chesapeake Bay Submerged Aquatic Vegetation Habitat Requirements and Restoration Targets: A Technical Synthesis. EPA: Annapolis, MD.

De Lange, E. 1994. Manual for Simple Water Quality Analysis. International Water Tribunal (IWT) Foundation:Amsterdam.

Kennish, M.J. 1992. Ecology of Estuaries: anthropogenic effects. CRC Press: Boca Raton.

Klemm, D.J.. et al., 1990. Macroinvertebrate field and laboratory methods for evaluating the biological integrity of surface waters. EPA:Cincinnati, OH.

McDonald, B., W. Borden and J. Lathrop. 1990. Citizen stream monitoring, a manual for Illinois. Illinois Department of Energy and Natural Resources:Illinois.

Mitchell, M.K., W. B. Stapp. 1992. Field Manual for Water Quality Monitoring, an environmental education program for schools. GREEN:Ann Arbor, MI.

Phillips, D.J.H., P.S. Rainbow. 1993. Biomonitoring of Trace Aquatic Contaminants. Elsevier Applied Science: New York, NY.

Plafkin, J.L. M.T. Barbour, K.D. Porter, S.K. Gross, R.M. Hughes. 1989. Rapid Assessment Protocols for Use in Streams and Rivers: Benthic Macroinvertebrates and Fish. EPA: Washington, D.C. Rosenberg, D.M., V. H. Resh (eds). 1993. Freshwater Biomonitoring and Benthic Macroinvertebrates. Chapman & Hall:New York, NY.