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Corner of tab Bioassessment

Background & History



Photo of DEP workers sorting through dipnet samples at Cypress Creek In 1989, an innovative biological monitoring framework was published by EPA. This strategy consisted of two separate but inter-related components:

  1. Establishing new bioassessment protocols which combine biological sampling and analysis techniques into an integrated, multi-metric assessment with habitat evaluation; and
  2. Determining appropriate eco-regional reference sites which would be representative of a region's expected biological assemblage.

Once biological expectations are established, the biological community and habitat at a point of interest (a “test” site) is then compared to the regional reference condition, and the relative health of the system being evaluated may be determined.

To bring the new bioassessment approach to Florida, the Department initiated two major projects in early 1991. With funding provided by the Clean Water Act's Nonpoint Source Pollution grant program (Section 319), contracts were begun to delineate Florida's areas of ecological similarity (called ecoregions) and identify reference stream sites, and to refine EPA's biological (benthic macroinvertebrate) sampling methods to reflect Florida's freshwater stream systems.

Concurrently, the Department established its Biocriteria Committee to oversee the contracts and integrate the work into the agency's management programs. The Biocriteria Committee was composed of both technical and management staff from several divisions. The committee meetings also provided a venue for training and quality assurance activities to ensure statewide consistency in the implementation of the new approach. During method development, meetings were held four to five times per year, with various task forces established to handle pilot studies and research issues on separate occasions.

In 1993, the Regionalization Project for Florida delineated 13 sub-ecoregions  from 3 ecoregions as originally determined in the Ecoregions of the Conterminous United States (Omernik 1987) mapping project. Within nine of the regions, 85 stream reference sites were identified. The southernmost ecoregion, with its four subecoregions, was not included in the streams biocriteria development because the area is dominated by wetlands and canals, and natural streams are extremely rare.

After examining reference site data collected during five years of twice-yearly sampling, the nine ecoregions were collapsed into three bioregions, or areas of general homogeneity in the freshwater macrobenthic community. These bioregions split along the Panhandle, the Peninsula (excluding the Everglades Ecoregion) and Northeast Florida. Reference sites were then compared with sites receiving known pollution sources to determine differences in the macroinvertebrate community that resulted from anthropogenic pollution.

The products of this early streams bioassessment work included the seven-metric Stream Condition Index (SCI_1992, which generally scored between 7-33, depending on region and season) and the three-metric Bioreconnaissance (or BioRecon, which used a pass/fail assessment of 3 metrics). A standardized evaluation of habitat conditions is also performed at each site (Stream and River Habitat Assessment). For a complete description on the original SCI development, see Development of the Stream Condition Index (SCI) for Florida (1996). After using these indices for several years, FDEP became aware of more advanced methods to select metrics and calibrate biological indices, and embarked on a study to improve and recalibrate the early SCI and BioRecon.

In 2004, the Department re-evaluated the SCI and BioRecon metrics against an independent measure of anthropogenic impact, the Human Disturbance Gradient (HDG). Component metrics were reviewed and rescaled, lab processes were further standardized, and this work resulted in an improved SCI (SCI_2004, scored 0-100) and improved BioRecon (scored 0-10). For more information, see Stream Condition Index Report (Fore 2004). The SCI laboratory methods were slightly adjusted again in 2007 to increase the precision of the method. Rather than an analysis of one subsample of approximately 100 organisms, as in the SCI_2004, the SCI score is now generated as the average score of two subsamples of 150 organisms each (SCI_2007). At that time, the SCI was calibrated along the BioCondition Gradient, and an impairment threshold was proposed by an expert panel. See Stream Condition Index Report (Fore et al. 2007) for more information.


In 1998, Florida DEP began development of a lake bioassessment protocol to monitor and assess the biological integrity of Florida lakes using benthic macroinvertebrate communities. Lake geographic regionalization was based on topography, natural water chemistry, lake origin, lake hydrology and soils, and reference lakes were subsequently sampled in most regions. The regionalization process (described in detail in Griffth et al. 1996, Florida lake regions report. US EPA, Corvallis, OR) resulted in the delineation of 47 lake regions within Florida, although later analyses indicated that these regions could be aggregated, and that factors such as alkalinity (pH) and color were more accurate for distinguishing lake expectations. Data from 500 lakes were analyzed to examine relationships between macroinvertebrate communities, water quality parameters, and basin land use characteristics, leading to the development of the Lake Condition Index (LCI). Lake habitat assessments (recorded on the Lake Habitat Assessment Form (FD 9000-06) were performed in conjunction with LCI sampling. See Lake Condition Index Report (Tetra Tech 2000) for more information.

In 2006, the LCI was re-calibrated using the Human Disturbance Gradient (HDG) Approach. A total of 44 metrics were tested and none were significantly associated with the Landscape Development Index or habitat score. Macroinvertebrate response was overwhelmed by natural factors, such as pH and color (see Evaluation of Benthic Macroinvertebrates Assemblages as Indicators of Lake Condition, Fore 2007).

Because of the complications in assessing human disturbance in lakes using the invertebrate community, DEP subsequently developed methods involving the lake aquatic macrophyte community. Lake vegetation data were collected and evaluated against the HDG and several plant metrics were found to have a strong correlation with human disturbance. Four metrics were selected for the Lake Vegetation Index (LVI), a multi-metric tool which assesses lake health based on the plant community structure. The LVI is sampled per DEP SOP FS7320and calculated per DEP SOP LT7500. Florida DEP is currently using the LVI to assess human disturbance in lakes in Florida. The LVI method involves dividing a lake into 12 units and identifying plants 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 (double-sided rake on a rope) is deployed a minimum of five times during transect sampling to look for the presence of submersed aquatic plants. All plants for a unit are recorded in a single column on the Lake Vegetation Index Data Sheet (DEP form FD 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: Percent Native Taxa, Percent Invasive Exotic Taxa, Percent Sensitive Taxa, Dominant/Co-dominant Coefficient of Conservatism (C of C). For more information about the development of the LVI, see Lake Vegetation Index Report (Fore 2005). In 2007, a second index validation was conducted for the LVI, and it was calibrated against the Biological Condition Gradient. For more information, see Lake Vegetation Index Report (Fore 2007).


Florida DEP has developed, but not fully calibrated, biological monitoring tools for wetland ecosystems. A research team, led by Dr. Mark Brown of the University of Florida's Center for Wetlands, investigated potential wetland attributes for use in the development of biocriteria for these systems. The wetland biological assessment consists of vegetation transects, invertebrate 20 dipnet sweep sampling, and a qualitative periphyton sample collection. The University of Florida research team has developed a classification scheme for Florida’s wetland types and has completed a wetlands regionalization map. Wetland indices were developed for isolated herbaceous wetlands, isolated forested wetlands, and forested strands and floodplain wetlands (see documents on Bioassessment Publications. The Wetlands Condition Index for isolated herbaceous and forested wetlands have three components: a Wetlands Vegetative Index, a Wetland Macroinvertebrate Index and a Wetland Diatom Index. All three indices are strongly correlated with the LDI. For forested strands and floodplains, only a Wetland Vegetative Index was developed. These wetland bioassessment tools have been used to assess biological health in wetlands receiving wastewater.

Marine Bioassessment Program

FDEP has conducted exploratory studies and workshops for the development of estuarine and marine bioassessment tools (link to History of Bioassessment, marine activities). 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. Historical (1999) marine bioassessment work products include the following:

  1. Overview of previous bioassessment methods development - overview.pdf (PDF, 14kB)
  2. Report from habitat-based bioassessment workshop held April 1999 - habitatrpt.pdf (PDF, 1.5 MB)
  3. Summary and overview report for indicator-group workshops held fall 1998. Individual workshop reports are below - summaryrpt.pdf (PDF, 10 kB)
  4. Report from corals bioassessment workshop held October 1999 -  coralrpt.pdf (PDF, 25 kB)
  5. Report from submerged aquatic vegetation (SAV) bioassessment workshop held October 1999 -  savreport.pdf (PDF, 24 kB)
  6. Report from benthic macroinvertebrate bioassessment workshop held November 1999 - invertrpt.pdf (PDF, 29 kB)

Last updated: June 30, 2015

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