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Bioassessment Methods

Development and Application of DEP Bioassessment Methods

See our SOPS page to download SOPs and Forms identified below in bold italic type. 

Biological assessment provides a direct measure of designated use attainment for the vast majority of Florida’s surface waters, where the goal is propagation and maintenance of a healthy, well-balanced aquatic community. Because accurate assessment requires that the methods be customized for specific system types, Florida DEP has developed biomonitoring tools for streams, lakes and wetlands. The methods for streams (Stream Condition Index and BioRecon) and lakes (Lake Vegetation Index) have been comprehensively validated and calibrated using the process described below. While standardized sampling and interpretation methods for wetlands have been developed, they have not yet been fully calibrated. There exists a “biological integrity” determination in marine waters (measured as a 25% reduction in Shannon diversity); however, development of more sophisticated marine bioassessment methods is still in its infancy. Check this site periodically for updates on the development of these tools.


In 1993, the Regionalization Project for Florida delineated 13 sub-ecoregions from the 3 ecoregions originally determined in the Ecoregions of the Conterminous United States (1987) mapping project. Within 9 of the regions, stream reference sites were identified to establish biological expectations. The southernmost ecoregion, and its 4 sub-ecoregions, was not included in stream biocriteria development because of its unique ecological characteristics (typical streams are extremely rare; generally only canals and occasionally flowing wetland sloughs or strands are found in this area).

Using the recently developed 20 dipnet sweep technique, data was collected and analyzed from the ecoregions north of Lake Okeechobee. After examining data from five years of twice-yearly sampling, the 9 ecoregions were collapsed into 3 relatively homogeneous bioregions, consisting of the panhandle, the peninsula (excluding the Everglades Ecoregion) and northeast Florida.

The final products of Florida’s stream bioassessment development include the current ten metric Stream Condition Index (SCI) and the six metric Bioreconnaissance (or BioRecon). The SCI is the primary indicator of stream ecosystem health, identifying impairment with respect to minimally disturbed condition. The BioRecon is used as an initial watershed screening method to determine whether or not additional resources should be allocated to the area, such as sampling using the SCI method. A major recalibration of the SCI, using the Human Disturbance Gradient (HDG) and Biological Condition Gradient (BCG) approaches, occurred in 2007. To provide information for interpreting bioassessment results, a standardized evaluation of habitat conditions is performed concurrently with SCI and BioRecon sampling. For additional technical information about the development of the modern SCI and BioRecon tools, see Bioassessment Publications page.


The SCI is a composite macroinvertebrate index for use in flowing streams. Sampling consists of 20 dipnet sweeps of the most productive habitats found in a 100-meter stretch of a stream. DEP SOP SCI 1000 outlines the protocol to be used to sample an SCI for a watercourse. Organisms collected in these sweeps are preserved and brought back to the laboratory for processing in accordance with the DEP SOP SCI  2000. Data generated on the taxonomy and abundance of these organisms is used to calculate ten biological metrics, each of which has been shown to respond predictably to human disturbance. The metrics are:

  • Number of total taxa,
  • Number of long-lived taxa, those that require more than one year to complete their life cycle,
  • Number of Ephemeroptera (mayfly) taxa,
  • Number of Tricoptera (caddisfly) taxa,
  • Number of Florida sensitive taxa,
  • Number of clinger taxa,
  • Percent dominant taxon,
  • Percent Tanytarsini,
  • Percent very tolerant taxa,
  • Percent filterers.

The majority of these metrics decrease in response to adverse human influences, while two of the metrics (% dominant taxon and % very tolerant taxa) increase in response to human disturbance. Once the metrics are calculated, points are assigned for each metric based on criteria that have been regionally calibrated and are contained in DEP SOP SCI 2000. The points from each of these 10 biological metrics are then summed to determine an overall score of biological health, with scores of 64-100 considered “exceptional,” scores from 40 to 63 considered “healthy,” and scores of 0-39 considered “impaired.”

Stream Condition Index (SCI) Report - Fore, L. et al. 2007. Development and Testing of Biomonitoring Tools for Macroinvertebrates in Florida Streams. The statistical basis for SCI and Biorecon calculation SOPs.  

Development of Aquatic Life Use Support Attainment Thresholds for Florida’s SCI and LVI – DEP 2011

SCI Stressor Identification Process - DEP 2020. Describes natural and human-induced factors known to influence the SCI, and the process by which DEP evaluates which stressors are most likely to cause SCI failures. 


BioRecon is the initial screening tool for streams, intended to rapidly assess a site to prioritize it for more intensive sampling. The SOP for Performing BioRecons (DEP SOP FS 7410) differs from that for an SCI sample in that only four dipnet sweeps of the most productive habitats are performed. A Biorecon also differs from SCI sampling in that the organisms are sorted in the field using the BioRecon Field Sheet ( FD 9000-01) to target specific numbers of individuals for subsequent laboratory identification. Regionally based thresholds specific to this method have been established for each of 6 calculated metrics (a subset of the 10 metrics used in the SCI). The metrics in the BioRecon assessment, all of which decrease in response to human disturbance, include:

  • Number of total taxa,
  • Number of long-lived taxa, those that require more than one year to complete their life cycle,
  • Number of sensitive taxa,
  • Number of clinger taxa,
  • Number of Ephemeroptera (mayfly) taxa,
  • Number of Tricoptera (caddisfly) taxa.

The final Biorecon score is regionally adjusted and normalized to a range from 0 to 10 points. Scores of 6 to 10 are “exceptional,” scores from 4 to 6 are considered “healthy,” while scores below 3 indicate impairment.

Stream Habitat Assessment

Overall habitat quality is determined by measuring eight attributes known to have potential effects on the stream biota. DEP bioassessment protocols require a field habitat assessment at each stream site using DEP SOP FT 3100, which involves a mapping exercise (using FD 9000-04, see sample) and conducting a series of observations as specified in the Physical/chemical characterization SOP (DEP SOP FT 3001). Using all the information collected, each of the eight habitat parameters on the Field Habitat Assessment Form (FD 9000-05) is given a score (ranging from 1 to 20, with 20 being the highest quality).

The primary habitat parameters are:

  • Substrate Diversity - an indicator of the number of diverse, productive habitats (snags, logs, tree roots, aquatic vegetation, leaf packs [partially decayed], undercut banks, rock, or other stable habitat) present in a stream
  • Substrate Availability - an indicator of what percentage of the area of the stream bed is composed of productive habitats (as listed above)
  • Water Velocity - a valuation based on the maximum observed velocity of the stream at a typical transect, where higher velocities typically receive higher scores
  • Habitat Smothering - an indicator of the percentage of the area of the stream bed which is covered or "smothered" by sand or silt accumulation

The secondary habitat parameters are:

  • Artificial Channelization - a visual interpretation of the anthropogenic channelization of a stream based on its variance from natural stream patterns (sinuosity) and the presence of artificial bank structures
  • Bank Stability - a visual interpretation of the stability of a stream's banks based on evidence of erosion or bank failure
  • Riparian Buffer Zone Width - a valuation based on the estimated width of the riparian vegetative buffer on each side of the stream
  • Riparian Zone Vegetation Quality - a valuation based on: the percentage of riparian zone surfaces which are vegetated by native plant species; the presence of a variety of vegetative classes (trees, understory shrubs, herbs); evidence of community disruption (bare soil, mowing, vegetative harvesting)

The values assigned for each of these parameters are then averaged and assigned a rating corresponding to one of four categories (“optimal”: 120-160 points, “suboptimal”: 80 to 119 points, “marginal”: 40 to 79 points, and “poor”: 8 to 39 points).

Incorporation of Stream Assessment Tools into Program Areas

Several program areas use these bioassessment tools. Regulatory applications include:

  • Fifth Year Inspection (FYI) Program - the permitting program for domestic and industrial wastewater facilities
  • Status and Trends Monitoring - a combined probabilistic and fixed station monitoring program, where the data are analyzed and compiled into the Integrated Report, a report to the U.S. EPA on the status of Florida’s water resources.
  • Total Maximum Daily Load (TMDL) Program - a program which determines limits on pollutants for surface waters, and develops plans to reduce pollutants and prioritize watersheds for restoration
  • NPDES Stormwater, and Municipal Separate Storm Sewer System (MS4) Permits - programs which regulate industrial, construction-related, and publicly owned stormwater discharges.

Non-regulatory applications include:

Algae Methods

Florida DEP has developed two methods to assess periphyton communities, one for species composition and the other to estimate attached algal coverage. Algae respond to a number of stressors, making them potential early indicators of adverse aquatic change.

The Qualitative Periphyton Sampling SOP (DEP SOP FS 7220) is a method for the collection of algal community composition information from natural substrates. A total of 10 sample aliquots are apportioned across available habitats (snags, roots, leaf packs, vegetation and rock, excluding sediments) in a 100 m stream reach. To perform the method, a seasoned substrate is chosen, and algae is removed from a 9 cm diameter area and placed into a wide-mouth jar that was been filled with 100 mL of site water. Water and algae are mixed and a 4 mL aliquot is removed and placed into a centrifuge tube. Nine additional aliquots are sampled in this manner for a final volume of 40 mL. DEP used periphyton data collected using this SOP to attempt to develop the Stream Diatom Index.

Stream Diatom Index Development

In a process similar to that described for the SCI and LVI, DEP attempted to develop a periphyton assessment tool, the Stream Diatom Index (SDI), using a combination of the Human Disturbance Gradient (HDG) and Biological Condition Gradient (BCG) approaches. Unfortunately, the diatoms appear to be very strongly influenced by pH (as well as conductivity and color), which confounds the periphyton community response to human disturbance, including nutrient enrichment effects. The SDI does not appear to clearly or predictably respond to objective measures of human disturbance, currently making it an unreliable tool for assessing adverse human effects on stream systems. DEP has much additional work before periphyton community composition may be used as a reliable bioassessment tool. (Final SDI Report)

Development of Aquatic Life Use Support Attainment Thresholds for Florida’s SCI and LVI – DEP 2011

Rapid Periphyton Survey

The Rapid Periphyton Survey (RPS) (conducted per DEP SOP FS 7230) quantifies the extent and abundance of algae in a 100 m stream segment. Nine observations are made every 10 m for a total of 99 observations (11 transects, including 0 and 100 m marks). A canopy measurement is made at the mid-point of each transect using a spherical densiometer. A small handful of substrate is haphazardly collected at each transect point and is visually examined for the presence/absence and for the type of algae (filamentous, diatom, or other). The average thickness is measured perpendicular to the substrate and this noted on the Rapid Periphyton Survey field sheet ( FD 9000-25). When sufficient data are collected using the RPS method, DEP intends to establish an RPS threshold that indicates where the algae interfere with the designated use of a waterbody.


Florida DEP has developed lake bioassessment protocols to monitor and assess the biological integrity of Florida lakes. Initial geographic regionalization resulted in the delineation of 47 lake regions within Florida (Griffth et al. 1996. Florida Lake Regions Report. US EPA, Corvallis, OR). Although an early Lake Condition Index (LCI) was developed by comparing reference lakes to non-reference lakes, subsequent efforts in 2007 to recalibrate the LCI using the Human Disturbance Gradient (HDG) concluded that the LCI was not well-correlated with adverse human effects because macroinvertebrate response was overwhelmed by natural factors (see Evaluation of Benthic Macroinvertebrates Assemblages as Indicators of Lake Condition).

Lake Vegetation Index

Because of the complications in assessing human disturbance in lakes using the invertebrate community, DEP developed methods involving the lake aquatic macrophyte community resulting in the Lake Vegetation Index (LVI), a multi-metric tool which assesses lake health based on the plant community structure. Four LVI metrics were chosen based on an HDG evaluation, and the LVI was subsequently calibrated via the BCG process. DEP currently uses the LVI as the primary method to assess biological health in Florida lakes. The LVI is sampled per DEP SOP LVI 1000 and calculated per DEP SOP LVI 2000 The LVI method involves dividing a lake into 12 units and identifying plants to the lowest possible taxonomic level in 4 of the 12 units. Plants are identified in each unit by a visual boat “drive by” and also via a transect approach. A frodus is deployed a minimum of five times during the transect to assess the presence of submersed aquatic plants. All plants for a unit are recorded in a single column on the Lake Vegetation Index Data Sheet (FT 9000-27) and a dominant or co-dominant is assigned based on areal extent. Unknown plants are brought back for expert identification and verification. The sampling season for the LVI is May through October. Data generated on the presence of species is used to calculate four biological metrics — each of which has been shown to respond to human disturbance. The metrics are:

  • Native Taxa
  • Invasive Taxa
  • Sensitive Taxa
  • Dominant Coefficient of Conservatism (C of C)


Florida DEP has concluded the initial development of biological monitoring tools for wetland ecosystems. A research team, led by Dr. Mark Brown of the University of Florida's Center for Wetlands, investigated attributes from multiple biological assemblages in wetlands for use in the development of biocriteria for these systems. The wetland biological assessment tools consists of vegetation transects, 20 dipnet sweeps for macroinvertebrates, and a qualitative periphyton sample collection. The University of Florida research team developed a classification scheme for Florida’s wetland types and also completed a wetlands regionalization map. The Wetland Condition Index has three components: a Wetland Vegetative Index, a Wetland Macroinvertebrate Index and a Wetland Diatom Index. All three indices are strongly correlated with the LDI. Wetland indices were developed for isolated herbaceous wetlands, isolated forested wetlands, and forested strands and floodplain wetlands (documents available through Report Search Page). DEP ultimately plans to calibrate these indices using the BCG approach.

Marine Communities

DEP has conducted exploratory studies and workshops for the development of estuarine and marine bioassessment tools. While the previous attempts have not yielded practical results, DEP is currently planning studies for further development, potentially including an evaluation of epi-benthic taxa and fish in a variety of habitat types.

Last Modified:
November 23, 2020 - 3:10pm

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