Sampling and Use of the Stream Condition Index (SCI) for Assessing Flowing Waters: A Primer

October 24, 2011 1 DEP-SAS-001/11

Sampling and Use of the Stream Condition Index (SCI) for 

Assessing Flowing Waters: A Primer

FDEP 

Standards and Assessment Section

Bureau of Assessment and Restoration Support

DEP-SAS-001/11

October 24, 2011
Sampling and Use of the Stream Condition Index (SCI) for Assessing Flowing Waters: A Primer

October 24, 2011 2 DEP-SAS-001/11

Contents

Contents 2

1. Introduction 3

2. How Objectives Affect SCI Sampling Decisions and Interpretation 9

3. Water Level and the SCI 30

4. Overview of SCI Sampling Process 36

5. SCI Training 41

6. SCI Data Usability 42

7. SCI Training Materials, Training Requirements, and Checklists 46

8. Literature Cited 46
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1. Introduction

The Stream Condition Index (SCI) is a biological assessment procedure that measures 

the degree to which flowing fresh waters support a healthy, well-balanced biological 

community, as indicated by benthic macroinvertebrates. The BioRecon is a companion 

tool to the SCI, which provides screening level information. For both the SCI and 

BioRecon, the principles in this document must be followed for successful application of 

the methods. In addition to the concepts presented in this document, samplers, data 

analysts, and resource managers who use the SCI (or BioRecon) must also read DEP SOP 

SCI 1000 and BRN 1000, for the training, quality assurance, sampling, laboratory, and 

index calculation Standard Operating Procedures. Furthermore, those wishing to 

implement and interpret the SCI must also read and understand “Development of 

Aquatic Life Use Support Attainment Thresholds for Florida’s Stream Condition Index 

and Lake Vegetation Index” (DEP-SAS-003/11).

Because multiple natural and anthropogenic factors affect biological results (Figure 1), it 

is critical that SCI users fully understand the method to ensure any conclusion regarding 

potential human environmental effects are scientifically defensible. 

Figure 1. Many factors affect biological community composition. To conclude that 

human disturbance is primarily responsible for biological degradation, reasonable 

knowledge of the influence of natural factors is essential.

1.1. SCI Samplers Must Exercise Best Professional Judgment

Only an experienced, qualified SCI sampler is able make the difficult field decisions 

necessary for proper application of the method. Field staff must be absolutely confident 

they fully understand the objectives of the sampling to enable these necessary field 

decisions. Samplers should NOT be burdened by undo pressures to sample when 
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conditions are not appropriate for the method and objective (e.g., there should NOT be 

a binding contract that stipulates collecting a specific number of samples by a certain 

date, even if conditions are not appropriate). Additionally, samplers must collect 

sufficient meta-data (e.g., water level, habitat, photographs) to document, and assist 

with determining the usability of a given SCI result for a particular purpose or objective

(see section 6 below).

1.2. Maintaining Linkages between SCI and Important Related Data 

Because many factors affect aquatic biota and the SCI results, it is imperative that all 

associated data (flow conditions, habitat scores, other physical factors affecting a site, 

etc.) be linked to the SCI results, so that a determination may be made that each sample 

is, or is not, consistent with the study objectives. There is a high likelihood that 

indiscriminate use of SCI scores, in the absence of these associated data, will result in 

inappropriate or incorrect environmental decisions. It is the responsibility of the staff 

and managers analyzing the data and making environmental decisions to fully 

understand the complexities associated with the SCI scores and to use the data 

appropriately. Samplers must also assist data analysts and managers in the 

determination that SCI results are, or are not, appropriate for a given objective.

1.3. Summary of the Development of SCI Metrics

DEP considered a diverse array of community attributes (Figure 2) and used the Human 

Disturbance Gradient approach to objectively select metrics that respond to human 

influences in a predictable manner (Fore et al. 2007). The Human Disturbance Gradient 

is composed of four factors:

• The Landscape Development Intensity Index (Brown and Vivas 2004);

• Habitat Assessment scores (DEP SOP FS 3000);

• Hydrologic Modification Index; and

• Water column ammonia concentration.

These components, described in detail by Fore et al. (2007), were converted into a 

dimensionless index, with low values denoting low disturbance and increasing values 

associated with more intense human influences. The Human Disturbance Gradient was 

used as the x-axis for testing a wide variety of biological attributes associated with the 

measurement of ecological integrity (Figure 2). Figure 3 depicts the absolute value of 

correlation coefficients (Spearman’s r) for a variety of biological attributes against the 

HDG. Once an attribute is demonstrated to respond predictably to human influence, it 

is termed a metric. The 10 selected attributes metrics were chosen to:

• Represent as many attribute categories as possible;

• Provide meaningful and predictable assessment of human effects; and
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• Avoid redundancy if several correlated metrics were providing similar 

information.

Figure 2. Major attribute categories, and example metrics, for determining biological 

integrity.

Figure 3. Correlation between various metrics and the Human Disturbance Gradient. 

Arrows indicated metrics selected for the SCI, and associated attribute group.

1.4. The 10 SCI Metrics
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A description of the ten metrics is presented here. When aggregated into the SCI, these 

provide a comprehensive and robust assessment of stream biological health. 

• Percent Tanytarsini 

Tanytarsini midges are sensitive to disturbance, so the metric was included in the SCI as 

the best available measure of the chironomid assemblage, which is an important group 

in stream invertebrate communities. 

• Number of Sensitive Taxa

Lists of sensitive and very tolerant macroinvertebrates were established by analyzing 

the responses of individual species to the HDG (Fore et al. 2007a). The number of taxa 

selected as sensitive equaled around 12% of the taxa tested. Many sensitive species 

belonged to the Ephemeroptera, Trichoptera or Odonata; several chironomids were also 

included. All the Plecoptera were included as sensitive taxa (Figure 4).

Figure 4. Response of the number of sensitive taxa metric to the HDG. The photo is of a 

plecopteran (stonefly).

• Percent Very Tolerant Taxa

The number of very tolerant taxa was approximately 10% of the taxa tested. The 

percent very tolerant individuals were highly correlated with the HDG (Figure 5). 

Figure 5. Response of the percent very tolerant metric to the HDG. Photos are of 

lunged snails and tolerant midges.
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• Number of Total Taxa 

• Number of Ephemeroptera Taxa

• Number of Trichoptera Taxa

The number of different types of organisms present and the richness of the Trichoptera 

(caddisflies) and Ephemeroptera (mayflies) have historically been shown to decrease 

with human disturbance. Figure 6 depicts the response of the number of 

Ephemeroptera taxa to human disturbance, which is similar to the response of the 

Trichoptera taxa and total taxa metrics. These three measures were chosen since each 

metric may respond differently, depending on the type of disturbance (e.g., mayflies are 

more sensitive to metals, certain caddisflies may be more sensitive to flow disruption). 

Figure 6. Response of the Ephemeroptera metric to the HDG. The photo is of 

Tricorythodes, a sensitive mayfly.

• Percent Dominant Taxon

Substantial shifts in proportions of major groups of organisms, compared to reference 

conditions, may indicate degradation. The percent dominant taxon, which increases in 

conditions where a few pollution tolerant organisms are very abundant, to the exclusion 

of other taxa, was selected as a metric. 

• Percent Filterers or Suspension Feeders

Disruption of food webs has long been associated with human influence, especially 

organic pollution. Of the functional feeding group measures, the relative abundance of 

filterers or suspension feeders (percentage of filterer individuals) had the highest 

correlation and most consistent relationship with the HDG (Figure 7). Filter feeders 

extract nutrients by straining food particles from the water column. If the water flow or 

quality of the organic matter in the water is compromised, a reduction in filter feeders 

will occur.
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Figure 7. Response of the percent filter-feeder metric to the HDG. The photo is of a netspinning caddisfly.

• Number of Long-Lived Taxa

Voltinism refers to the number of distinct reproductive cycles for a given organism that 

may take place in a year. Long-lived taxa included semi-voltine insects and non-insects 

that require greater than one year to complete their life cycles. Long-lived taxa richness 

would be expected to decrease if a disturbance event (e.g., sporadic illegal dumping, 

periodic pulses of chemicals from rain events) occurred at a site within a year of sample 

collection (Figure 8).

Figure 8. Response of the long-lived taxa metric to the HDG. The photo is of a mollusk, 

the threatened purple bank climber. 

• Number of Clinger Taxa

Clingers are those taxa morphologically adapted to hold onto substrates during routine 

flow conditions and would be expected to decline as humans alter a stream’s 

hydrograph (e.g,. channelization), especially during abrasive events caused by high 

stormwater inputs from impervious surfaces. Clinger taxa richness was highly 

correlated with the HDG (Figure 9).

Human disturbance gradient

 

 

Human disturbance gradient

 

 
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Figure 9. Response of the clinger taxa metric to the HDG. The photo is of a damselfly 

larvae.

2. How Objectives Affect SCI Sampling Decisions and 

Interpretation

It was mentioned previously that biota respond to natural and human stressors alike 

(Figure 3). It is imperative the study objectives associated with each SCI sample are 

clearly articulated and that efforts are taken to control for confounding factors that may 

interfere with the appropriate interpretation of the SCI scores. Although there may be 

multiple factors to consider, the main three issues to be aware of during an SCI study 

are:

• existing and antecedent flow conditions, 

• habitat conditions at a given site, and 

• water quality, especially human degradation of water quality (such as exceeding 

water quality criteria).

Potential uses of the SCI and other environmental measurments, in context of DEP 

program decisions, are mentioned below and interaction of these components and their 

effects on score interpretation is discussed.

2.1. Water Quality Investigations for the Watershed 

Assessment/Total Maximum Daily Load Program and for 

Determining a Causative Pollutant

 

 

 

 
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The objective for an impaired waters assessment/causative pollutant identification 

study is to decide if water quality issues are adversely affecting biological health. To list 

a waterbody on the verified list of impaired waters, DEP must reasonably demonstrate 

the pollutant responsible for poor SCI scores. Since water flow significantly affects 

stream biota, the investigator must first determine if the existing and antecedent flow 

conditions were appropriate for sampling. It may seem obvious, but aquatic organisms 

will die if a site goes dry. If desiccation has occurred within the past 6 months of a 

sampling event, the recent dry conditions, not water quality, may dominate the 

invertebrate response. The SCI SOP contains a provision that SCI sampling be 

postponed for 6 months after a site has gone completely dry (with no refugia for 

organisms) and then has begun flowing again, before sampling (although additional 

information on this issue, including use of site specific information, is provided in 

section 3 below). This wait will help ensure that desiccation was not the most 

prominent factor influencing the SCI score. Similarly, stream organisms are rheophyllic 

(“flow loving”). If water velocity is very low (standing water, stagnant conditions), it is 

very likely to adversely affect the assemblage of organisms, even if water quality is 

excellent. Therefore, sampling for impaired waters assessments/causative pollutant 

identification purposes shall be conducted during periods when water velocity has been 

0.05 m/sec or greater for at least 28 days (one month). Controlling for these water flow 

issues (not sampling during inappropriate conditions) will help minimize the influence of 

desiccation and water velocity on the SCI results.

Additionally, habitat conditions significantly affect macroinvertebrate communities. 

Since the objective of an impaired waters assessment /causative pollutant identification 

study is to isolate water quality factors causing degradation, efforts should be taken to 

establish sites where habitat is not a substantial factor limiting potential biological 

health. This means that the investigator must establish sampling sites (where possible) 

in stream reaches with adequate substrate diversity and availability, intact stream 

morphology (little or no artificial channelization), adequate flow, and optimal riparian 

buffer zones. Figure 10 shows an example of a site where habitat and hydrology are 

significant adverse influences, meaning that an alternate site in the stream segment 

should be selected for SCI sampling, if one is available. If the entire stream reach has 

habitat and hydrological limitations and funding for restoration is not available, 

reclassification to a Class III-Limited category should be considered (as described in 

Chapters 62-302.400 and 62-302.800, F.A.C. Note that deleterious sediment input may 

result in habitat smothering, and that restoration would involve upland erosion control 

and other Best Management Practices.
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Figure 10. A site where habitat and hydrology significantly and adversely influence the 

biological community, meaning that an alternate site in the stream segment should be 

selected for SCI sampling (if possible) during an impaired waters assessment /pollutant 

identification study. If habitat and hydrological limitations occur throughout the entire 

stream reach, and funding for restoration is not available, reclassification to a Class IIILimited category should be considered. 

Specific conductance (conductivity) is a water quality parameter worthy of special 

discussion. Elevated conductivity at a site may be due to its proximity to natural saline 

conditions (e.g., at tidally influenced systems) or due to human sources. The SCI was 

designed for freshwater streams, and as such, it would not be appropriate to use the 

tool where conductivity is naturally elevated (e.g., near estuarine areas). However, if a 

human discharge has artificially elevated a stream’s conductivity, the SCI may be used to 

document the resulting potential adverse community response. One must take care to 

assess the source of the conductivity when deciding the appropriateness of the SCI.

In conclusion, if flow and habitat limitations are controlled for during an impaired 

waters assessment /causative pollutant identification study, and sufficient water quality 

data are collected, the water quality factor(s) responsible for any observed biological 

degradation are more effectively identified.

2.2. Point Source Studies

Point source studies involve an evaluation of effluent quality and whether existing 

permit limits are sufficient to maintain surface water quality standards (62-302.530,

F.A.C.) and prevent degradation of the biological communities in the receiving waters. 

To assess the influence of the discharge, an upstream-downstream SCI study is routinely 

employed, while controlling for important variables (e.g., habitat) between the 

upstream (control) and downstream (test) sites. Selection of similar habitats from areas 

of similar water velocity is important to determine if the effluent is associated with any 

changes in the SCI scores. Additionally, the use of replicate sampling stations, for both 
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control and test sites, will better characterize the variability of the biological data. If 

reductions in the SCI scores occur between the control and test sites, the intra-site 

variability and the magnitude of the change should be assessed, as well as potential 

categorical shifts. 

2.3. Best Management Practices (BMPs) Effectiveness Studies 

Previous studies on the effectiveness of forestry best management practices, using the 

SCI, followed a typical Before-After-Control-Impact design. This design may be 

applicable to other BMP studies. Stream reaches were selected where neither flow, 

habitat, or water quality were limiting to aquatic communities. An upstream “control 

site” and a downstream “test site” were established, and both were sampled (with 

replicates) prior to the onset of the human activities (conducted with BMPs). Sampling 

continued at the same control and test sites after the potentially damaging human 

activities (with mitigating BMPs) had taken place and SCI scores were compared, both 

pre- and post- disturbance (see Figure 11). In this particular case, Analysis of Variance 

indicated that no significant differences between the control and test sites had occurred 

after the forestry activities, demonstrating that the BMPs were effective in protecting 

stream biota .

Figure 11. SCI results of a Before-After-Control-Impact study assessing the effectiveness 

of forestry Best Management Practices. “C” and “T” mean control and test sites, 

respectively. Note that a different version of the SCI was used during the time period, 

but the concepts apply to the current SCI.

2.4. Stream Restoration Studies
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The objectives for a stream restoration study are to determine if one or all the following 

factors have been improved or mitigated in a manner that adequately supports aquatic 

communities:

• Stream morphology; 

• Habitat; 

• Water supply to the stream and in-stream water velocity ; and

• Water quality.

The investigator shall measure each of these important variables over time, along with 

conducting SCI sampling. This will enable a demonstration that the restoration activities 

can be successfully linked with a positive biological response (improving the SCI score as 

the desired environmental endpoint). Past studies of reclaimed streams in mining areas 

have suggested that all four factors listed above need to be adequately addressed to 

ensure a positive biological response. It is important that data collected as part of a 

restoration study not be indiscriminately used for unintended purposes (e.g., placing a 

waterbody on the verified list impaired waters list when habitat, not water quality, was 

the limiting issue).

2.5. Minimum Flow and Levels Studies

As mentioned above, sufficient water flow is critical to stream biological community 

health. Biological communities will be negatively affected when humans adversely 

modify watershed hydrology or artificially reduce water inputs to a stream (leading to 

extended dry or stagnant conditions). However, care must be taken to distinguish 

between effects of natural droughts and the similar effects caused by human reductions 

in water quantity. Also, if a study design calls for using SCI sampling after stream 

desiccation (e.g., within 6 months) or during periods of stagnant water velocities (not 

generally appropriate for conducting the SCI SOP), it is important that the resulting data 

(probable SCI failures) not be misinterpreted as water quality issues (see section on 

maintaining associated data with the SCI below).

2.6. Integrated Water Resource Monitoring (Status and Trends) 

Program

The Integrated Water Resource Monitoring program (IWRM, aka Status and Trends) is a 

monitoring program designed to determine the quality of Florida’s fresh surface and 

ground waters at a large scale, using two differing approaches. The first (Trend 

network) is a fixed-point monitoring program that is designed to determine changes in 

water quality over time at 76 set locations around the state. The sampling locations 

were selected to capture the quality of waters that flow into the state, and at the 

bottom of watershed basins (determined using a Hydrological Unit Code, [HUC]). Rivers, 

streams, and one spring are monitored as part of the program. Water samples are 

collected monthly at all surface water Trend sites, and the SCI is conducted annually.
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The second component of the program uses a random stratified (probabilistic) sampling 

network, called the Status monitoring network. The objective of the Status network is 

to provide an estimate of water resource conditions within the state for surface and 

ground waters. Because of the extent of aquatic resources within the state, no one 

sampling network could adequately sample all waters in Florida each year due to 

logistical and practical limitations. The probabilistic design was selected to balance 

resources, provide a scientific and statistically sound platform, and provide coverage of 

waters at a reasonable scale. A subsample of the water resource is selected, collected 

and analyzed during a specified sampling window referred to as a “sampling period.” 

The design is based on a set geographic boundary, or reporting unit (“zone”) that 

follows the Water Management District boundaries. 

The SCI tool was adopted as part of the Impaired Waters Rule listing process and was 

incorporated into use by the IWRM program in both the Status and Trend monitoring 

networks in 2004. 

To assist samplers in making the decision whether to sample SCI at a particular site for 

the IWRM program, the following rules have been developed:

• Do not sample if the system is not functioning as a stream or river (it is 

more like a lake, estuary, wetland, marsh, prairie, canal, ditch, etc.);

• Do not sample if the system is currently dry or disconnected, or has been 

completely dry within 6 months prior to the site visit. If this cannot be 

determined with confidence, do not sample;

• Do not sample if flood conditions exist and water levels are > 0.5 meters 

above normal;

• Do not sample if the system is tidally influenced (regardless of 

conductivity values);

• Do not sample if the system is a spring run with conductivity values > 600 

μmhos;

• Do not sample if the average velocity is < 0.05 m/s or has been < 0.05 m/s 

in 28 days prior to the site visit. If this cannot be determined with 

confidence, do not sample;

• Do not sample if conditions are unsafe; and

• Do not sample in the South Florida Bioregion (south of Lake 

Okeechobee).

The assumption was made at the onset of the use of the SCI tool in the IWRM program 

that it applied to all Class III freshwaters. Many of the Class III waters within the central 

and southern region of the state have been hydrologically altered or have been created 

for the primary purpose of flood control. Canals and ditches, even if they are connected 

to waters of the state, are currently excluded for sampling because they are not 

functioning as a stream or river. 
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Due to the random design of the probabilistic network, samples are collected only 

where the site is specifically selected, based on a 1:100,000 scale map. This results in 

sites being selected in areas that are possibly not optimum habitats, but should be 

representative of the stream or river resources in the reporting unit. The objective, as 

stated above, is to characterize the condition of waters within a zone. The intent is not 

to characterize any specific stream or river. Therefore, when results are reported, they 

pertain only to the estimate of condition of representative resources within the zone. 

For the Status Network, the designated water quality sampling point must remain within 

the 100-meter Habitat Assessment (HA) and SCI stretch, but the stretch may be 

positioned upstream (water quality sampling point at the zero marker) or downstream 

(water quality sampling point at the 100 marker) as necessary in order to provide the 

most representative stretch.

For the Trend network, samplers are permitted to orient the 100 meter stretch 

upstream or downstream from the water quality sample collection point as necessary in 

order to provide the most representative habitat stretch for the system. The designated 

water quality sampling point does not have to reside within the 100-meter stretch, but 

it must be no farther than 200 meters away from the HA stretch. However, if moving 

the HA stretch 200 meters away still does not meet the acceptable criteria for 

performing the HA/SCI, do not perform the HA/SCI.

2.7 Use of the SCI and Measures of Floral Health to Assess Achievement 

of Nutrient Standards

This section describes the evaluations conducted by DEP to assess whether a stream 

attains the narrative nutrient criterion in Rule 62-302.530(47)(b), F.A.C., pursuant to the 

provisions in Rule 62-302.531(2)(c), F.A.C. This approach evaluates water chemistry and 

biological (flora and fauna) and physical information from the waterbody to determine if 

nutrient concentrations are causing an imbalance in flora or fauna in a given stream. 

Because of the complexity associated with nutrient enrichment effects, no single 

assessment tool is adequate to evaluate all potential impacts, and instead, a weight-ofevidence evaluation must be conducted. 

This section discusses:

• The nutrient enrichment conceptual model for streams;

• The process for numerically interpreting the narrative nutrient criterion in 

streams;

• Available procedures for evaluating the floral community in the stream, including 

chlorophyll a levels, periphyton abundance and species dominance (as measured 

using the Rapid Periphyton Survey [RPS]), and nuisance macrophyte distribution 

(as measured using the Linear Stream Vegetation Survey [LVS]); 
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• Evaluating the faunal community in the stream using the Stream Condition Index 

(SCI) or BioRecon; 

• Efficiently collecting the information during one sampling event; and

• Examples of a weight-of-evidence approach for determining achievement of 

nutrient criteria.

2.7.1 Nutrient Enrichment Conceptual Ecological Model for Streams 

Nutrients are naturally present in aquatic systems and are necessary for the proper 

functioning of biological communities. Nutrient effects on aquatic ecosystems are 

moderated in how they are expressed by many natural factors (e.g., light penetration, 

hydraulic residence time, presence of herbivore grazers and other food web 

interactions, and habitat considerations). As a result, determining the appropriate 

protective nutrient regime is largely a site-specific undertaking, requiring information 

about ecologically relevant responses. 

To evaluate ecosystem health, it is important to acknowledge that adverse nutrient 

enrichment effects follow a conceptual ecological model (Figure 12). When 

anthropogenic nutrient loading or concentrations exceed a system’s assimilative 

capacity, the primary response consists of changes to the primary producer 

communities (periphyton, phytoplankton, or vascular plants), and excess production of 

plant biomass. In turn, this enhanced floral biomass could lead to habitat loss (e.g., from 

excess periphyton smothering or nuisance plant biomass accumulation), food web 

alterations (e.g., dominance of taxa that thrive in nutrient/organic matter enriched 

conditions), and/or low dissolved oxygen (DO) from decomposition of plant biomass or 

respiration. This chain of events is ultimately reflected in meaningful biological 

endpoints, such as excessive algal mats, excess water column chlorophyll a, excess 

nuisance vascular plant growth, and/or failing Stream Condition Index (SCI) scores. 

These adverse biological endpoints constitute imbalances of aquatic flora and/or fauna. 
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Figure 12. Simplified nutrient enrichment conceptual model used to assess potential 

adverse effects of nutrients on aquatic life and human uses in streams. Relationships 

between nutrients and biological responses are highly influenced by site-specific and 

mitigating factors.

Conversely, if data show that biological health is fully supported in an aquatic system 

(no adverse responses consistent with the ecological model), it may be concluded that 

the associated nutrient regime is inherently protective of the waterbody, and the 

narrative nutrient criterion is achieved. 

When conducting nutrient studies, it is important that sampling locations and other 

environmental conditions (canopy cover, habitat, water depth and flow, etc.) are 

determined to be representative of the system and that water quality data be collected 

in the same waterbody segment as the biological monitoring stations. The stations shall 

be established in a manner consistent with the study design concepts described in the 

document titled Development of Type III Site Specific Alternative Criteria (SSAC) for 

Nutrients (DEP-SAS-004/11).

2.7.2 The Process for Numerically Interpreting the Narrative Nutrient Criterion in 

Streams

The narrative nutrient criterion in Rule 62-302.530(47)(b), F.A.C., states that “in no case 

shall nutrient concentrations of a body of water be altered so as to cause an imbalance 

in natural populations of aquatic flora or fauna.” The method for numerically 

interpreting this narrative nutrient criterion, on a site-specific basis, is provided in Rule 
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62-302.531, F.A.C, using a hierarchical process (Figure 13). This hierarchical scheme 

specifies a prioritization for determining the numeric nutrient criteria that apply to a 

given waterbody. Beginning at the top of Figure 13, if there is a Total Maximum Daily 

Load (TMDL), Site Specific Alternative Criterion (SSAC), Water Quality Based Effluent 

Limitation (WQBEL), or other DEP-approved action involving nutrients for a waterbody 

(e.g., Reasonable Assurance derived values), one of these would be the applicable 

nutrient criteria. If not, values based on cause-effect relationships between nutrients 

and biological response (i.e., springs and lakes) would apply. If no cause-effect 

relationship has been established, such as is the case for Florida streams, referencebased Nutrient Thresholds, used in conjunction with biological information, become the 

applicable interpretation of the narrative nutrient criterion. If none of the above are 

available, then the narrative nutrient criterion continues to apply to the waterbody, 

which could be numerically interpreted on a site-specific basis.

If a site specific interpretation has not been established for a stream, reference streambased Nutrient Thresholds (Table 1, Figure 14), combined with information on aquatic 

flora and fauna, are used to interpret the narrative nutrient criterion.

Figure 13. The hierarchy for numerically interpreting the narrative nutrient criterion.

Table 1. Reference stream-based Nutrient Thresholds.

Nutrient Region Total Phosphorus 

Threshold

Total Nitrogen 

Threshold

Panhandle West 0.06 mg/L 0.67 mg/L 

Panhandle East 0.18 mg/L 1.03 mg/L 
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North Central 0.30 mg/L 1.87 mg/L 

Peninsula 0.12 mg/L 1.54 mg/L 

West Central 0.49 mg/L 1.65 mg/L 

South Florida No numeric nutrient threshold. The narrative 

criterion in paragraph 62-302.530(47)(b), 

F.A.C., applies. 

Figure 14. Map of stream Nutrient Regions.

These stream Nutrient Thresholds, which are the same as those promulgated by EPA 

(http://water.epa.gov/lawsregs/rulesregs/florida_index.cfm) are based on:

• The 90th

• The 75

percentile data distribution of rigorously verified, minimally disturbed 

streams in the Panhandle West, Panhandle East, North Central, and Peninsula 

regions; and

th

Note that stream Nutrient Thresholds do not apply in South Florida.

percentile data distribution of biologically healthy streams (those with 

an average score of >40 on the Stream Condition Index [SCI]) in the West Central 

Region. 
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It is important to recognize that the method for deriving the Nutrient Thresholds 

directly results in the expectation that some of Florida’s biological healthy streams will 

exceed the Thresholds. It is for this reason, and because nutrient thresholds may not be 

appropriate for every Florida waterbody, that Rule 62-302.531, F.A.C., contains a 

provision, described below, that allows use of biological information to fully evaluate 

achievement of the criterion.

For streams, if a site specific interpretation pursuant to paragraph 62-302.531(2)(a) 

(TMDL, SSAC, Level II WQBEL or RA Plan) has not been established, Nutrient Thresholds 

are used to interpret the narrative nutrient criterion in combination with biological 

information. The narrative nutrient criterion in paragraph 62-302.530(47)(b), F.A.C., 

shall be interpreted as being achieved in a stream segment if: 

• Information on chlorophyll a levels, algal mats or blooms, nuisance macrophyte 

growth, and changes in algal species composition do not indicate an imbalance in 

flora or fauna; AND EITHER

• The average score of at least two temporally independent SCIs performed at 

representative locations and times is 40 or higher, with neither of the two most 

recent SCI scores less than 35 (i.e., no faunal imbalances), OR

• The Nutrient Thresholds (expressed as annual geometric means) in Table 1 are 

not exceeded more than once in a three year period.

In cases where the Nutrient Thresholds are exceeded but there are no imbalances in 

both aquatic flora (phytoplankton, periphyton, vascular plants) AND fauna (invertebrate 

community), the narrative criterion is achieved. DEP has developed techniques to 

measure both flora and fauna, as described below, to determine when there is, or is not, 

an imbalance. Many of these evaluations can be conducted during the SCI sampling 

exercise. DEP continues to explore methods for gathering this type of biological 

information in aquatic systems. To stay informed of DEP bioassessment efforts, visit our 

website at: http://www.dep.state.fl.us/water/bioassess/index.htm

.

2.7.3 Evaluating Stream Flora: Attached Algal Communities

DEP conducted a comprehensive study of stream periphyton in Florida in an attempt to 

formulate a multi-metric index for assessing human disturbance, including nutrient 

effects (see Development of a Stream Diatom Index). Preliminary analysis indicated that 

the best potential metrics were percent sensitive diatom cells, percent tolerant diatom 

cells, percent diatom cells that prefer high oxygen, percent cells that prefer oligotrophic 

conditions, and van Dam’s weighted index for trophic status. These metrics were 

transformed into a dimensionless index, the Stream Diatom Index (SDI). Unfortunately, 

further analysis showed that the SDI was most highly correlated with pH. When the 

data were categorized according to pH, a relationship between SDI and human 
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October 24, 2011 21 DEP-SAS-001/11

disturbance was not observed. Based on these findings, DEP determined that the SDI is 

not appropriate for use as biocriteria due to its poor correlation with

human disturbance and its strong association with pH, meaning that other methods for 

assessing stream floral health were needed. 

DEP has also investigated using a modification of EPA’s Rapid Periphyton Survey (RPS) to 

quantify the extent (coverage) and abundance (thickness) of attached algae 

(periphyton) and found that the RPS was an effective tool to demonstrate a lack of 

abundance of nuisance or problematic algal growth. In subsection 62-303.200(10), 

F.A.C., a nuisance species is defined as “...species of flora or fauna whose noxious 

characteristics or presence in sufficient number, biomass, or areal extent may 

reasonably be expected to prevent, or unreasonably interfere with, a designated use of 

those waters.” 

To conduct the RPS method, a trained biologist surveys a 100 meter segment of a 

stream or river by establishing 11 transects across the waterbody at 10 meter intervals, 

and determining the presence and thickness of algae at 9 points along each transect, for 

a total of 99 sampling points. Additionally, a densiometer measurement to determine 

canopy coverage is taken near the center of each transect. The following ranks are used 

to quantify algal thickness:

• “0” = algae are absent (a rough surface with no algae). 

• “1” = algae less than or equal to 0.5 mm OR no algae visible but 

surface is slimy (including muck and biofilm), 

• “2” = greater than 0.5 mm to 1 mm, 

• “3” = greater than 1 mm to 6 mm, 

• “4” = greater than 6 mm to 20 mm, 

• “5” = greater than 20 mm to 10 cm, and 

• “6” = algae greater than 10 cm. 

In DEP’s experience, if a high percentage of the stream is covered by relatively thick 

algae (RPS rank > 4), there may be adverse effects on the stream. Therefore, if the 

percentage of sampled points with a thickness rank of 4-6 is 20% or greater, the 

biologist collects a composite sample of the dominant groups of periphyton in the 

stream segment for lab identification of the dominant algal taxa. If autecological 

information is available for the dominant taxa, this is also qualitatively evaluated. Two 

determine persistence, two temporally independent RPS are routinely conducted. 

Rank 4-6 periphyton growth is naturally observed at minimally disturbed Nutrient 

Benchmark streams and at streams that have healthy SCI scores (> 40). Nutrient 

Benchmark streams had Landscape Development Intensity Index (LDI) values < 2, no 

point source discharges, optimal habitat, and were subjected to a comprehensive field 

evaluation by DEP scientists to ensure that they were minimally disturbed by humans. 

DEP is currently conducting a comprehensive analysis of RPS data to determine how the 

RPS correlates with water chemistry, the Stream Condition Index (SCI), and independent 

measures of human disturbance such as the LDI. Preliminary analysis of RPS data 
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October 24, 2011 22 DEP-SAS-001/11

collected at 467 RPS sites statewide, including RPS collected at the Nutrient Benchmark 

streams used to derive stream Nutrient Thresholds and at other biological healthy sites, 

yields the information described below. 

RPS rank 4-6 coverage at Nutrient Benchmark streams ranged from 0% to 66%, with a 

mean value of 6% and a 90th percentile value of 25%. RPS rank 4-6 coverage at all 

biologically healthy sites (as indicated by stream condition index scores > 40), ranged 

from 0% to 91%, with a mean value of 8% and a 90th percentile value of 32%. Therefore, 

if a stream exhibits RPS rank 4-6 percent coverage between the mean percent observed 

at these minimally disturbed and healthy sites (6-8%) and the associated 90th percentile 

values (25-32%), this would be considered an indication of no imbalance of flora. DEP 

also considers the persistence of periphyton coverage during this evaluation (see 

examples in section 2.7.8 below).

Both DEP and EPA used a change point in RPS algal coverage (expressed as persistent 

coverage of RPS rank of > 4) as a line of evidence to link nitrate enrichment to adverse 

biological effects when deriving the springs nitrate criterion (Figure 15). 

Figure 15. The relationship between persistent Vaucheria percent cover (coverage of 

RPS rank of > 4) was a line of evidence used to develop the 0.35 mg/L nitrate-nitrite 

criterion in Florida springs. 

2.7.4 Evaluating Stream Flora: Vascular Plant Communities
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October 24, 2011 23 DEP-SAS-001/11

Another line of evidence to determine if streams are healthy is relative lack of nuisance 

macrophyte growth by certain vascular plant taxa that may interfere with designated 

uses of a waterbody. The Linear Vegetation Survey (LVS) is a rapid assessment tool for 

evaluating ecological condition based on vascular plants. To employ the LVS method, a 

trained biologist surveys a 100 meter segment of a stream, divides the stretch into 10 

meter sampling units, and identifies the plant species present to the typical high water 

mark, including submersed, floating, and emergent plants. The sampler then

determines the dominant or co-dominant species by estimating the 1 or 2 species with 

the largest areal extent. It is also possible to have no dominance or co-dominance, in 

which case, no dominant is assigned. Note that quantitative mapping of vascular plant 

communities is also part of the Habitat Assessment process.

To assess the community composition (including sensitive taxa), the LVS takes into 

account each plant species’ Coefficient of Conservatism (C of C) score (assigned by 

expert botanists as part of a DEP initiative in 2011) that indicates the plant’s specific 

habitat requirements. Plants with higher C of C scores have the most fidelity to high 

quality, unaltered sites, while a plant with a score of 0 displays no such fidelity, and 

includes invasive exotic species listed by the Florida Exotic Pest Plant Council (FLEPPC). 

For a list of C of C scores, FLEPPC taxa, and other vascular plant attributes relevant to 

the LVS, see DEP SOP LVI 1000 Appendix LVI 1000-1. 

FDEP reviewed the available LVS results for the minimally disturbed reference streams 

used by EPA for nutrient criteria development in Florida. Because many streams 

naturally have very little or no vegetation, interpretation of LVS data requires that a 

minimum of 2 m2 of macrophyte coverage be present throughout a 100 m stream reach. 

DEP evaluated LVS data from 58 reference sites and found that 19 of these sites had 

sufficient plant growth (> 2 m2) to further evaluate the LVS data. Based on these data, if 

a site’s average C of C score is greater than or equal to 2.5, the plant community 

composition may be considered to be part of the reference site distribution. Similarly, 

this analysis showed that if frequency of occurrence of FLEPCC exotics at a site is less 

than or equal to 25% of the total plant occurrences, the site may be considered to be 

part of the reference site distribution. Therefore, if a stream exhibits a C of C score > 2.5 

and the frequency of occurrence of FLEPCC exotics is < 25% of the total plant 

occurrences, this would be considered an indication of no imbalance of flora. However, 

it is important to acknowledge that invasive exotic species can occur even in the 

absence of nutrient impacts. Care should be taken to avoid incorrectly concluding that 

any occurrence of exotic plants is an imbalance of flora caused by nutrients.

2.7.5 Evaluating Phytoplankton/Chlorophyll a Data

During development of the Impaired Waters Rule (Chapter 62-303, F.A.C.), DEP solicited 

expert input on ecological effects of chlorophyll a on streams from a panel of Florida 

scientists. This expert panel concluded that annual average stream chlorophyll a values 
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October 24, 2011 24 DEP-SAS-001/11

exceeding 20 ug/L constitutes evidence that aquatic life uses were not fully supported. 

DEP uses this value, expressed as an annual average not to be exceeded, as an 

impairment threshold in Chapter 62-303 F.A.C. However, neither the expert panel nor a 

review of stream chlorophyll a literature was able to identify a stream chlorophyll a

value below 20 ug/L that definitively did, or did not, support aquatic life uses. 

DEP also uses the presence of persistent phytoplankton blooms as an indicator of floral 

imbalances. An unacceptable phytoplankton bloom would consist of a situation where 

an algal species, whose noxious characteristics or presence in sufficient number, 

biomass, or areal extent may reasonably be expected to prevent, or unreasonably 

interfere with, the designated use of a waterbody. DEP evaluates the autecological 

information for the dominant bloom species, in conjunction with the associated 

chlorophyll a and the persistence of the bloom, as a line of evidence when assessing 

imbalances of flora. 

As part of the analysis, DEP also compares measured chlorophyll a values to the range of 

chlorophyll a concentrations that were observed at minimally disturbed Nutrient 

Benchmark streams and at streams that have healthy SCI scores (> 40). Nutrient 

Benchmark streams had Landscape Development Intensity Index (LDI) values < 2, no 

point source discharges, optimal habitat, and were subjected to a comprehensive field 

evaluation by DEP scientists to ensure that they were minimally disturbed by humans. 

Annual geometric mean chlorophyll a at the 94 Nutrient Benchmark streams used to 

derive stream Nutrient Thresholds ranged from 0.2 ug/L to 17 ug/L, with a mean value 

of 2.0 ug/L and a 90th percentile value of 3.2 ug/L. Annual geometric mean chlorophyll 

a at 274 biologically healthy sites (as indicated by stream condition index scores > 40), 

ranged from 1.0 ug/L to 19 ug/L with a mean value of 2.1 ug/L and a 90th percentile 

value of 3.5 ug/L. 

If a stream exhibits annual geometric mean chlorophyll a concentrations between the 

mean observed at these minimally disturbed and healthy sites (2.0-2.1 ug/L) and the 

associated 90th percentile values (3.2-3.5 ug/L), this would be considered a clear 

indication of no imbalance of flora. Conversely, if a stream exhibits annual geometric 

mean chlorophyll a values that exceed 20 ug/L, this is evidence of imbalances of flora. 

Streams with annual average chlorophyll values between 3.5 ug/L and 20 ug/L are 

evaluated on a site specific basis. DEP also considers the residence time, flow, 

climatological conditions, and size of the stream/river (i.e., stream order) when 

considering chlorophyll a expectations within this range. 

DEP additionally assesses chlorophyll a using a temporal trend test (a Mann’s one-sided, 

upper-tail test for trend, with a 95% confidence interval) in conjunction with the 

chlorophyll a impairment threshold. The observation of a statistically significant 

increase in chlorophyll a in a stream is another line of evidence used by DEP to 

determine floral imbalances.
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2.7.6 Evaluating Stream Fauna: SCI

As discussed earlier, the Stream Condition Index (SCI) is a biological assessment 

procedure that measures the degree to which flowing fresh waters support a healthy, 

well-balanced biological community, as indicated by benthic macroinvertebrates. Ten 

metrics that quantitatively describe stream community structure and function are 

summarized as a dimensionless index (the SCI), which scores between 0 and 100. DEP 

established a protective threshold SCI score based on a combination of the reference 

site data distribution and EPA’s Biological Condition Gradient approach (see 

Development of Aquatic Life Use Support Attainment Thresholds for Florida’s SCI and 

LVI – DEP, October 24, 2011).

DEP and EPA have concluded that a balanced faunal community is achieved if the 

average score of at least two temporally independent SCIs, performed at representative 

locations and times, is 40 or higher, with neither of the two most recent SCI scores less 

than 35. Attainment of the SCI threshold is an indication that the faunal community of 

the stream is not being adversely affected by nutrients to the extent that there is a loss 

in designated use. However, failure of the SCI threshold also does not mean that the 

stressor causing the loss of designated use is nutrients. Evaluation of other factors, as 

indicated by the nutrient enrichment model in 2.7.1 (including nutrient concentrations 

and floral communities) is useful information that could indicate nutrients are a factor. 

While the stressor may not be known, a failed SCI does indicate that fauna is not wellbalanced.

The BioRecon is a companion tool to the SCI with six metrics and a total score of zero to 

ten. A BioRecon score of 4 is equivalent to an SCI score of 40 (see Stream Condition 

Index (SCI) Report ). While BioRecon results may be considered as additional 

information, BioRecon should not be used as the only evidence (in the absence of SCI 

and other measures of floral health) to demonstrate attainment or nonattainment of 

biological health. 

2.7.7 Efficiently Conducting the RPS, LVS, Habitat Assessment (HA), and SCI

As adopted by reference in the Quality Assurance Rule (Chapter 62-160, F.A.C.), the 

Standard Operating Procedures (SOPs) for conducting the RPS, LVS, HA, and SCI 

methods are available at http://www.dep.state.fl.us/water/sas/sop/sops.htm:

• RPS: DEP SOP FS 7230; 

• LVS : DEP SOP FS 7320; 

• HA: DEP SOP FT 3100; and 

• SCI: DEP SOP SCI 1000.

Note that these SOPs are quite extensive, and that some include training and proficiency 

testing requirements and reference to the concepts presented elsewhere in this 
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October 24, 2011 26 DEP-SAS-001/11

document for establishing study objectives, including considerations for the selection of 

representative sites and environmental conditions (e.g., section 2.1 above). All these 

procedures require that an appropriate 100 meter section of stream be measured, with 

flags placed in 10 meter intervals. The following guidance provides a method to most 

efficiently conduct these SOPs in a semi-simultaneous manner:

1. Collect any water chemistry (e.g., nutrients, chlorophyll a, metered parameters) 

upstream of where biological sampling will occur prior to disturbing sediments;

2. Beginning at the downstream-most flag, measure the nine points for algal 

presence/thickness and record, as per the RPS SOP.

3. From this downstream-most flag, walk towards the next 10 meter flag and 

simultaneously perform the habitat mapping procedure while observing aquatic 

vascular plants (if present). Record both sets of observations according to the 

respective SOPs.

4. Continue steps 2 and 3 above until the upstream-most (100 m) flag is reached. If 

there is > 20% coverage of RSP rank 4-6, collect a representative sample of the algae for 

taxonomic identification. The RPS and LVS are now complete.

5. Complete the HA SOP based on the observations made during the habitat 

mapping exercise.

6. Conduct the SCI, sampling the observed habitats according to the SCI SOP. The 

data collection needed to evaluate the health of the flora and fauna is now complete.

These are current methods for evaluating flora and fauna in Florida streams. Measuring 

biology continues to be an evolving science. As improved methods are developed to 

evaluate information on chlorophyll a, algal mats or blooms, and excessive nuisance 

macrophyte growth, those should be integrated into the assessment.

2.7.8 Examples of a Weight-of-Evidence Approach for Determining Achievement of 

Nutrient Criteria 

As noted in the sections, there are currently no quantitative endpoints for the RPS and 

LVS. To evaluate whether a stream achieves the narrative nutrient criterion, the 

investigator must compile water chemistry data (e.g., Total Nitrogen [TN], Total 

Phosphorus [TP], chlorophyll a, and ancillary parameters such as color, turbidity, DO, 

pH, conductivity, and temperature, etc.) and a minimum of two of each of the following: 

RPS, LVS (if appropriate), HA, and SCI. Taken together, these data are used as multiple 

lines of evidence to decide whether a stream is healthy, with acceptable levels of 

nutrients. Examples of how DEP evaluates these multiple lines of evidence are provided 

in Table 2 and discussed below.
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Table 2. Examples of RPS, LVS, chlorophyll a, HA, and SCI data used to illustrate a 

multiple lines-of-evidence approach used by DEP for determining whether or not a 

stream exhibits imbalances of flora or fauna. In these examples, TP, TN, or both 

nutrients exceed the regional Nutrient Threshold values.

Measure Sample 

#

Stream

1

1

2 3 4 5 6

RPS (% Rank 4-6) 1 21 45 4 8 3 26

2 2 65 7 15 0 37

LVS

Avg. C 

of C

1 N/A 2.6 1.9 N/A 3.5 1.8

2 N/A 3.2 0.5 N/A 4.2 2.4

FLEPPC 

%

1 N/A 12 45 N/A 0 31

2 N/A 4 74 N/A 0 26

Chlorophyll 

(μg/L as annual 

geo. mean)

Year 1 17.2 1.1 NonDetect 4.5 3.5 1.3

Year 2 22.1 2.1 NonDetect 1.2 4.1 1.1

Habitat 

Assessment

1 121 109 105 133 81 110

2 113 102 98 126 77 107

SCI

1 45 44 39 67 22 42

2 39 33 29 58 31 39

1 In these examples, TP, TN, or both nutrients exceed the regional Nutrient Threshold values.

In Stream 1, although the RPS data showed a pulse of periphyton (which consisted of 

the non-problematic alga, Oedogonium), it was not persistent, meaning the RPS results 

were acceptable (see section 2.7.3). No plants were found in the water. However, an 

increasing trend was observed in annual chlorophyll a (using a Mann’s one-sided, uppertail test for trend, with a 95% confidence interval), and the chlorophyll values exceeded 

those typically observed in healthy streams. Although the SCI score was currently 

acceptable and habitat was not limiting, DEP concluded that the chlorophyll issue, 

following the conceptual model in section 2.7.1, was sufficient to judge that this stream 

has impaired flora. It is likely that the increased organic matter enrichment associated 

with the excess phytoplankton (as indicated by the chlorophyll) would eventually lead to 

faunal imbalances.

Stream 2 was characterized by significant algal smothering, as demonstrated through 

the RPS results. Taxonomic identification showed the algae community to be 

dominated by Lyngbya, a known nuisance species. Although the vascular plant 

community, as assessed using the LVS, was within the range of reference streams, and 
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chlorophyll a was non-problematic, the algal growth resulted in aquatic habitat 

smothering (a component of the HA), which likely led to the failing SCI score. DEP 

concluded that the RPS results, coupled with a poor habitat smothering score, was 

evidence that stream 2 has impaired flora, which in turn caused impaired fauna. These 

responses are consistent with the nutrient enrichment model in section 2.7.1.

Although periphyton and chlorophyll a were not issues in stream 3, the HA and LVS 

results showed that the invasive exotic vascular plant, Hydrilla was excessively 

abundant, leading to imbalances of flora. An increase in Hydrilla abundance was 

associated with reduced substrate diversity and failing SCI scores, meaning the elevated 

nutrient levels were associated with imbalances in flora and fauna, consistent with the 

nutrient enrichment model in section 2.7.1. This situation is complicated because 

invasive exotic plants can be observed even without nutrient enrichment. It is 

important to review other information, including the levels of nutrients in the 

waterbody that could contribute to species proliferation. In this circumstance, DEP 

concluded that excess nutrients exacerbated the floral community imbalances as 

evidenced by the LVS results.

Stream 4 is a minimally disturbed reference stream that was at the upper 98th percentile 

of the data distribution used to establish the regional Nutrient Threshold. The measures 

of both flora and fauna showed normal, healthy conditions, meaning that nutrient levels 

associated with the site are acceptable and the narrative nutrient criterion is achieved.

Floral measures at stream 5 were non-problematic, despite nutrient concentrations that 

exceeded the regional Threshold values. No primary or secondary nutrient responses, 

as described by the nutrient enrichment model in section 2.7.1, were observed, but the 

SCI indicated impaired fauna. The SCI results, combined with higher levels of nutrients, 

lead to the conclusion that the narrative nutrient criterion is not achieved. In this case 

however, habitat assessment results indicated artificial channelization, poor substrate 

diversity and availability, and a compromised riparian buffer zone. Observations also 

indicated extensive hydrologic modifications in the drainage basin. These habitat and 

hydrologic factors were evaluated as part of a TMDL process, prior to initiating a TMDL.

After an evaluation of all stressors (through a stressor identification study), habitat and 

hydrologic improvements were found to be the stressors affecting stream health, and 

not nutrient concentrations. DEP would then evaluate this stream under a site specific 

structure described in Rule 62-302.531, F.A.C.

In stream 6, both the RPS and LVS results suggested the early warnings of nutrient 

enrichment, with persistent periphyton coverage and changes in the vascular plant 

community, even though chlorophyll a and SCI results were acceptable. The periphyton

community was dominated by Vaucheria, a known nuisance species, while the vascular 

plants, Alternanthera philoxeroides and Panicum repens (two FLEPPC exotics), were 

moderately abundant. Habitat assessment results indicated moderate smothering by 

the periphyton and a reduction in substrate diversity associated with the exotic plant 
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October 24, 2011 29 DEP-SAS-001/11

growth. DEP concluded that this was sufficient evidence of floral imbalances, which if 

allowed to continue without intervention, would also result in faunal imbalances, as 

predicted by the nutrient enrichment model in section 2.7.1.

In conclusion, the information presented in this section, including the examples, provide 

a multiple lines of evidence approach to numerically interpret the narrative nutrient 

criterion, on a site-specific basis, as provided for in Rule 62-302.531(2)(c), F.A.C.

2.8 Use Attainability Analyses and Class III-Limited Reclassifications

Chapters 62-302.400 and 62-302.800, F.A.C., describe the requirements to reclassify 

Class III waterbody to a Class III-Limited waterbody. For any downgrade, a Use 

Attainability Analysis (UAA) must be conducted, as explained in the document, Process

for Reclassifying the Designated Uses of Florida Surface Waters (DEP-SAS-001/10). The 

Class III - Limited category is restricted to waters shown to be wholly artificial or altered 

through dredging to the extent the physical characteristics of the waterbody limit its 

ability to support aquatic life use. 

The following is a summary of these requirements.

A petitioner must present appropriate and scientifically defensible water quality, 

biological, hydrological, and habitat studies and analyses, as well as environmental, 

social, and economic studies to demonstrate that: 

• None of the uses being removed are existing uses;

• The uses to be removed would not be attained by implementing effluent limits 

required by Sections 301(b) and 306 of the Federal Clean Water Act in 

conjunction with implementation of cost-effective and reasonable best 

management requirements for nonpoint source pollution control;

• The proposed reclassification is clearly in the public interest; 

• Water quality standards in downstream waters will be fully protected; and

• One or more of the criteria from Paragraph 62-302.400(11)(c), F.A.C., apply. This 

portion of the rule, based on 40 CFR 131.10(g), allows removal of a designated 

use that is not an existing use, as defined in § 131.3, or establishment of subcategories of a use if the State can demonstrate that attaining the current 

designated use is not feasible because: 

1. Naturally occurring concentrations of substances prevent the 

attainment of the use;

2. Natural, ephemeral, intermittent or low flow conditions or water 

levels prevent the attainment of the use, unless these conditions may be 

compensated for by the discharge of sufficient volume of effluent discharges 

without violating State water conservation requirements to enable uses to be met;
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3. Human caused conditions or sources of pollution prevent the 

attainment of the use and cannot be remedied or would cause more 

environmental damage to correct than to leave in place;

4. Dams, diversions, or other types of hydrologic modifications preclude 

the attainment of the use, and it is not feasible to restore the waterbody to its 

original condition or to operate such modification in a way that would result in the 

attainment of the use;

5. Physical conditions related to the natural features of the waterbody, 

such as the lack of a proper substrate, cover, flow, depth, pools, riffles, and the 

like, unrelated to water quality, preclude attainment of aquatic life protection 

uses; or

6. Controls more stringent than those required by sections 301(b) and 

306 of the Federal Clean Water Act would result in substantial and widespread 

economic and social impact.

Because a downgrade to the Class III-limited category is restricted to physically and 

hydrologically altered waterbodies, biological sampling should occur in areas 

representative of these human stressors. Consequently, the waterbody segment will 

likely be habitat limited and the hydrologic modifications may be such that the 

waterbody is frequently dry or not flowing. Although both of these conditions would 

likely prevent the waterbody from supporting a healthy biological community, it is 

appropriate to sample SCI and other biological measures under these obviously 

stressed conditions because it is consistent with the study objectives (see example in 

section 3 below).

3. Water Level and the SCI

All scientific methods have limitations that must be understood to effectively use the 

technique for making valid decisions. As previously mentioned, aquatic organisms will 

die if a site goes dry. For pollutant identification studies (including nutrient studies),

wait a minimum of 6 months after a completely dry site has begun flowing again before 

considering sampling, unless site specific information is available that indicates a 

particular stream invertebrate community recovers more quickly than 6 months (e.g., 3-

4 months). In these situations, sampling may occur after the suitable time period has 

elapsed that allows for biological recolonization from the desiccation event. For 

example, if the investigator has the necessary taxonomic skills, exploratory dip net 

sweeps may be conducted and the organisms field identified to determine the degree of 

recovery from the dry conditions. If it appears that a typical stream community is 

present, the investigator may commence sampling, documenting the reasons behind 

the decision. 

Routinely, SCI sampling can be performed only within approximately 0.5 m of the 

water’s surface (the arm length of an average sampler). It is imperative that the 
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October 24, 2011 31 DEP-SAS-001/11

sampler be confident that the “reachable” habitat in this top 0.5 m has been fully 

inundated with water for a minimum of one month (28 days) prior to sampling (Figure 

16). If water level at a site increases into this reachable zone to the extent that the 

sampler is not confident that the accessible habitats were inundated, the sampler 

should wait a minimum of 28 days to allow time for stream organisms to colonize the 

formerly exposed habitats. Similarly, if a site did not go completely dry, but stopped 

flowing and contained a series of disconnected pools for some time period, samplers 

should wait at least 28 days after flow has commenced (with a minimum water velocity 

of > 0.05 m/sec), before sampling. Note that it may take longer than 28 days for 

organisms to re-inhabit previously dry substrates and for rheophyllic organisms to 

recolonize stagnant reaches, depending on site characteristics. Avoid sampling sites 

after these low water level/stagnant events until sufficient time passes to eliminate 

these water level effects as confounding factors in interpreting the SCI results. If there 

is doubt about a particular sampling event, samplers should communicate with data 

analysts to flag the SCI results as potentially being affected from these water level 

issues. 

As an example, Figures 17 and 18 depict a recent increase in water level that would limit 

a sampler’s ability to collect organisms from the previously wetted and colonized 

substrate. When conditions such as these are encountered, the sampler must have 

sufficient knowledge and training to abort SCI sampling. Understanding hydrographs 

from streams in the general area (not every stream has a gauge) and extrapolating that 

information to the study stream is extremely valuable for determining when sampling is, 

or is not, appropriate. Smaller streams typically have more spikes in their hydrographs, 

where the water level rises quickly and significantly but then returns to “normal” levels 

within days (Figure 19). A valid SCI sample can be collected when the formerly 

colonized habitats may be reached; however, it is important that samplers exercise 

caution to make sure that the substrates selected for sampling have been appropriately 

inundated.

Figure 16. Schematic cross section of a stream showing recent increases in water levels 

indication the SCI sampling should not be conducted.
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In streams with natural geomorphology and sinuosity, the habitats targeted for SCI 

sampling act as refugia from scouring during flood events, and sampling may be 

conducted when inundated substrates are reachable. However, in channelized systems 

there may be significant scouring after routine rain events. Depending on the study 

objectives, sampling may be conducted after a rain event in a channelized system to 

demonstrate the adverse effects of hydrological modification on the system. All SCI 

samplers must fully understand how water levels affect their ability to collect a valid, 

meaningful SCI sample, and abort sampling when conditions are not suitable. The 

following examples will help illustrate this concept. 

Figure 17. Stream water level two weeks prior to scheduled SCI sampling.
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Figure 18. Stream level on day SCI was scheduled to be performed. Note that reachable 

substrates were dry on the previous photo. SCI sampling should be aborted when these 

conditions occur.

Figure 19. Hydrograph showing times when substrates are reachable.

Example 1, TMDL Sampling 

A sampler is collecting SCI data to determine if water quality degradation (in this case, 

nutrient enrichment) is sufficient to list a waterbody on the verified list of impaired 

waters. When arriving at the site, the sampler determines that almost all of the 

productive habitats (roots, snags, leaf packs) are exposed to air due to extremely low 

water levels (see Figure 20). Hydrographs from nearby streams indicate these low 

water conditions have occurred for the past few months. Water velocity in the stream is 

not measureable (0.00 m/sec). Should the sampler collect the SCI? No, the conditions 
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are such that the lack of inundated habitat and adequate velocity are the dominant 

factors affecting the stream biota. Collecting the SCI and attributing the low scores to 

poor water quality is not scientifically defensible, as factors other than water quality 

were highly influential.

Figure 20. Photo of low water conditions resulting in the desiccation of the majority of 

viable stream habitats. SCI sampling for TMDL/pollutant identification studies should 

not be conducted under these conditions. 

Example 2, MFL Sampling

A study is attempting to establish a relationship between water quantity in a stream and 

the SCI scores with the hypothesis that more water yields higher scores. Water levels in 

the stream rose by one meter during the past week. The sampler notes that terrestrial 

vegetation is currently under water and reachable substrates in the top 0.5 m (snags, 

limerock) have no “slimy” feel. Should the sampler collect the SCI? No, the recent 

increase in water level means the organisms have not yet colonized the accessible 

substrates. Sampling under these conditions would erroneously produce data indicating 

reductions in SCI scores with increased water delivery.

Example 3, Impaired Waters Assessment/Pollutant Identification Sampling

Due to heavy rains, a stream has water levels two meters over its banks into the riparian 

floodplain (see Figures 21 and 22 for photos of typical and flooded conditions). This 

condition has occurred for four weeks. The sampler notes that there is no access to the 

actual stream channel due to the water depth, but some habitat in low velocity 

backwaters of the floodplain can be reached. Should the sampler collect the SCI? No, 

the actual stream cannot be sampled. The few organisms that may have colonized the 
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low velocity backwaters of the floodplain would not be representative of the actual 

stream health. Again, collecting the SCI and attributing the low scores to poor water 

quality is not scientifically defensible, as factors other than water quality were highly 

influential. Note: in a large stream or river where the water lever has risen significantly 

(greater than 0.5 m) but not out of its banks, an SCI can be collected as long as the 

proper incubation period has occurred (minimum of 28 days). 

Figure 21. Typical flow conditions at a sampling site. 

Figure 22. Flow conditions at the same site shown in Figure 21, associated with a high 

water event, including floodplain inundation, when SCI sampling would not be 

appropriate.

Example 4, Sampling for Use Attainability Analyses
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An entity is proposing to sample a series of severely hydrologically modified systems, 

including canals and urban ditches, as part of a Use Attainability Analysis to reclassify 

the systems into the Class III-Limited category, as described in Chapters 62-302.400 and 

62-302.800, F.A.C. Although the canals do not typically go dry, the hydrologic 

modifications are such that the canals are characterized by consistently low water 

velocity (< 0.05 m/sec), except for during flood events. Can the canals be sampled for 

SCI under typical conditions? Yes, because the defined objective is to determine if the 

hydrologic modifications (and corresponding habitat limitations) have interfered with 

the development of a healthy community, the investigator may sample during the 

typical velocity conditions, even if they are below 0.05 m/sec. Similarly, the urban 

ditches in the study rarely contain water for more than 3 or 4 months, and are usually

dry during the remainder of the year. Again, because the study objectives are to 

determine the influence of the hydrologic modifications, it is appropriate for the 

investigator to sample the ditches after they contain water for the typical maximum 

amount of time, even if that is only 3 or 4 months.

4. Overview of SCI Sampling Process

Fundamental to SCI sampling is the selection of the best available habitats, in the 

optimal flow, to collect the indicator organisms in the areas they typically inhabit. This 

was the manner by which all the reference and potentially disturbed sites for calibrating 

the SCI were sampled. If the “healthy” organisms are not found in their optimal living 

quarters (best habitat and flow) one may conclude that some disturbance (human or 

natural) was responsible for their absence. A pristine stream, if not sampled according 

to the SCI protocol (e.g., if one erroneously sweeps only sand or low velocity 

backwaters), will assuredly fail the SCI. Conversely, if the very best habitat and flow 

conditions are sampled in accordance with the SOP in a human-damaged system, the 

SCI result will accurately reflect the level of disturbance. Therefore, training and ethics 

of SCI samplers is very important. A biologically healthy site, if sampled poorly, will fail 

the SCI. A disturbed site with an impaired community will also fail, even when sampled 

with a bias toward the best available habitats, but due to environmentally relevant 

reasons, not as a sampling artifact. Samplers must thoroughly understand the concepts 

associated with the Standard Operating Procedures (SOPs), and consistently follow the 

SOPs, and operate in an ethical manner to prevent sampling errors (see DEP SOP SCI

2100.

4.1. Sampling Site Selection and System Classification

First, the study objectives must be clearly understood, and a 100 m segment of stream 

that is appropriate to address the objectives should be selected as a sample site. For 

purposes of site selection, it is important to understand there are variations in a 

stream’s flow, habitat and biota as it moves through the landscape, and this variability 
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has great implications for the proper application of the SCI. Within a single reach of a 

stream or river, there are areas of higher and lower densities and diversities of 

macroinvertebrates. These differences occur both on the local scale (i.e., different 

qualities of in-stream habitats; snags vs. muck in a 100 m section) and the landscape 

scale (i.e., different flow regimes and habitat diversity over a 5-10 mile section of 

stream). 

For defining DEP’s inherent biological expectations associated with the SCI, stream or 

river segments that generally had flow (with velocities ranging from 0.05 m/sec to 0.4 

m/sec except during seasonal droughts or floods) and typical “stream” habitats were 

selected. In other words, the SCI should be applied to streams that have similar and 

comparable characteristics to those streams used in the calibration data set. 

Comparing biological communities from swamp-like, lake-like or tidally-affected 

segments of streams to the biological expectations established for “typical” streams is 

not scientifically defensible. Proper classification of the system type one is attempting 

to sample is another fundamental concept for appropriate application of the SCI. 

However, it should be noted that the SCI may be used to assess human alterations in 

habitat and hydrology via a logically designed study.

Over a short distance, a stream may change from a system with a well-defined natural 

channel, good flow, and an abundance of habitats to a forested swamp with little to no 

defined channel and very little perceivable flow. If the system is behaving like a swamp, 

and not a flowing stream in that specific area, one would not expect the swamp-like 

segment to perform well on the SCI. Conversely, if a study is attempting to assess the 

detrimental effects of stream impoundment, it may be appropriate to sample a former 

stream segment that has been hydrologically modified to resemble a lake, because such 

sampling is consistent with the study objectives. Also, consider large rivers that become 

very wide with dramatic reductions in flow as they transition toward an estuarine 

situation. This area of the “river” may actually be acting more like a very low velocity, 

flow-through lake, or may be tidally influenced. Sampling these types of areas may 

result in inappropriate SCI failures, because of incorrect system classification (comparing 

“apples” to “oranges”). Example photos of sites unsuitable for the SCI method are 

provided in Figures 23, 24, and 25.
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Figure 23. Example of swamp conditions present, indicating that the SCI is 

inappropriate at this site.

Figure 24. Example photo of lake conditions present, indicating that the SCI is 

inappropriate at this site.
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Figure 25. Example photo of tidal influence, meaning SCI is a not an appropriate tool.

Thus, atypical areas not representative of the stream reach should be avoided when 

using the SCI as an indicator of biological integrity, unless the study objectives dictate 

otherwise. For example, unless the study objectives are to determine adverse habitat 

effects of road construction, sampling directly adjacent to or under a bridge (usually 

disturbed by channelization) should be avoided, as this area would not be 

representative of the stream reach. 

4.2. Appropriate Antecedent Hydrologic Conditions

Water levels should be examined as outlined above to determine if conditions are 

appropriate for the purpose of the study (see section 3 above). Samplers must be 

careful to consider how long habitats in the top 0.5 m of the surface have been 

inundated. If the habitats have been recently dry, they should not be sampled. This is 

most important when sampling large rivers where water levels can rise over 0.5 m 

without being easily observed. For larger systems, data from stage height recorders are 

typically available and the resulting hydrograph should be carefully examined to 

determine when conditions are appropriate for sampling. Samplers must develop 

intimate familiarity with the hydrology of streams in their regions and learn to 

extrapolate the information from available hydrographs to nearby streams to determine 

if antecedent hydrological conditions were appropriate.

4.3. Optimal Habitat Selection
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Once it’s been decided the hydrologic conditions are suitable for the objectives of the 

study, the sampler must identify the best available habitats where the 

macroinvertebrates actually reside. This is accomplished by performing the habitat 

assessment procedures to determine the types and quantity of substrates present (see 

FT 3000, found at: http://www.dep.state.fl.us/water/sas/sop/sops.htm ).

The dip net sweeps are apportioned by determining the number of productive habitats 

(roots, woody debris, leaf material, macrophytes or rock) present with a surface area 

greater than 2 m2

• The invertebrate taxa important for calculating many of the SCI metrics (e.g., 

sensitive taxa, Trichoptera, Ephemeroptera, filter feeders) are rheophyllic, 

meaning they prefer areas with higher water velocity, which also often translates 

into areas with higher effective concentrations of dissolved oxygen and food 

availability. Therefore, leaf packs (leaves caught on snags above the substrate) 

that are in the main flow are preferred over leaf mats (leaves on the bottom), 

which tend to be associated with lower velocity and potential anaerobic 

conditions. Additionally, snags, roots, macrophytes and rocks in the flow are 

better habitats than the snags, roots, etc. in lesser flow or backwater areas.

(see SOP). When targeting specific substrates to sample in particular 

areas of the stream (best available habitats), samplers should keep in mind how 

macroinvertebrates use the substrates. It is important to “think like a bug”. Some 

examples are:

• Organisms use the substrates as refugia from predators (e.g., fish, other 

invertebrates) and as a place to feed. Fine fibrous roots are preferred 

substrates, since they have more surface area and therefore more areas to hide, 

when compared with larger diameter roots. Similarly, snags with softer, 

deteriorating bark have more hiding places and attachment points for organisms 

(e.g., net spinning caddisfly filter feeders, hellgrammites) than fresh, smooth 

snags (e.g., cypress knees). This makes the deteriorating snag with many 

crevices a much preferred habitat. Similarly, jagged rocks with a rough 

architecture (i.e., with nooks and crannies) are preferred over smooth rocks.

• Since aquatic organisms need to live in the water, habitats that are constantly 

inundated with water are preferred over ones that go dry. For example, 

samplers should focus on the types of aquatic macrophytes that can survive long 

periods of inundation rather than those species which typically may be exposed 

to air for long periods. When terrestrial plants are seen submerged in a stream, 

it is a “dead giveaway” that the water level at a site has recently increased, and 

depending on the magnitude of the increase, aborting the trip should be given 

serious consideration.

4.4. Sampling Technique

Another important aspect of the SCI concerns the sampler’s ability to actually remove 

the organisms from the substrates and properly collect them into the dip net. Samplers 
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absolutely must provide sufficient agitation of substrates to dislodge the organisms, and 

ensure that all organisms are captured (into the net) without loss. Based on this guiding 

principle, here are important sampling technique issues to be aware of:

• The opening of the dip net should always be placed perpendicular to the flow 

and the net should be placed downstream of any agitation so that organisms 

flow into the net. 

• When agitating the substrate, the material (water, detritus, plus organisms) 

should be directed into the mouth of the dip net, using hands or a brush (scrub 

INTO the net, not parallel to it). Similarly, the substrates should be agitated very 

close to (or inside of) the dip net to avoid loss of organisms. For example, roots, 

remove-able rocks and snags, and submersed macrophytes should be agitated 

inside the bag of the dip net, where large snags, rocks, macrophytes, and sand 

should be sampled as close to the dip net opening as possible. 

• Leaf pack material should be placed directly into the net and the organisms 

dislodged “one leaf at a time” before discarding excess leaves. It is critical that 

there be NO LOSS of organisms during any field reduction of leaf material.

• It is important to vigorously shake and scrape all surfaces of the habitats at least

• When sampling sand, penetrate the sand with fingers, to approximately 2 cm 

deep, and using a pulling motion, draw the organisms from the sand into the 

waiting dip net. Feel for partially buried bivalves and ensure they are placed in 

the net.

3 times, while having the net situated in a manner such that no organisms are 

lost. 

• For leaf mats, only sample the top 2 cm to avoid the anoxic layers below. 

Large rivers can be sampled from the bow of a boat (best for reachable snags in 

deep areas) or by wading along the shoreline. The applicability of the SCI to 

large rivers is described in the Stream Condition Index (SCI) Report. Although 

some portions of rivers may have un-wadeable water depths, the SCI sampling is 

conducted only on the reachable habitats (top 0.5 m) in the system, thus 

minimizing effects of depth.

• When sampling streams or large rivers, be particularly sure that the sampled 

habitats are in areas of adequate water velocity (not in a backwater area) and 

have been sufficiently inundated.

5. SCI Training 

5.1. Field Sorting as a Training Tool

Field sorting at reference sites is a useful activity for a “sampler-in-training” to learn 

whether their selection of habitats and dip netting techniques are effective for capturing 

macroinvertebrates. After a sampler chooses a particular habitat and samples it, they 

should bring the contents of the net to the stream bank, and using a white tray, sort 

through the material searching for organisms. Before sorting, the material in the net 
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should be thoroughly rinsed with site water to eliminate turbidity. During sorting, only a 

small amount of material should be placed into the tray with about a centimeter of site 

water, so that approximately half of the white background is visible. Samplers should 

systemically search the tray and using forceps and pipettes, remove organisms for 

additional examination with a hand lens. Samplers must become familiar with the basic 

orders and families of aquatic macroinvertebrates, as outlined in DEP SOP SCI 2230. 

Although there are many comprehensive taxonomic guides, a useful field book for 

beginners is “A Guide to Common Freshwater Invertebrates of North America”, by J. 

Reese Voshell, Jr., published in 2002 by the McDonald and Woodward Publishing 

Company, Blacksburg, Virginia. During field sorting, the sampler should compare the 

relative diversity of taxa found in individual sweeps taken from various habitats and flow 

regimes. This type of systemic examination will provide immediate feedback regarding 

the degree of success associated with the sampler’s field decisions.

5.2. Apprenticeship

Because of the complexities mentioned above, DEP requires that novice sampling staff 

undergo a systematic training /apprenticeship program. The goal of the training is to 

produce SCI samplers able to demonstrate the necessary critical thinking skills and 

sampling technique required by the SOP. Training shall consist of numerous field visits 

(minimum of 12) at a variety of sites (starting at reference sites, followed by disturbed 

sites) and different water levels, where novice staff receives instruction from the 

experienced staff (who have passed the SCI audit) on the concepts presented here. As 

training progresses, the novice staff should gradually demonstrate the required best 

professional judgment and sound sampling technique (see below for training checklists). 

Once training has been completed, a field audit with the Standards and Assessment 

Section to assess a sampler’s ability to adhere to the SOPs may be scheduled.

6. SCI Data Usability

The intent of this section is to provide a procedure for how Stream Condition Index (SCI) 

data will be used for DEP environmental decisions.

Determining if data are usable for a particular purpose is a complex task, requiring a 

logical and balanced evaluation of many factors. The procedural components of the SCI

assessment must be performed by staff with sufficient scientific expertise and 

demonstrated proficiency, as mandated by Rule 62-160, F.A.C. Additionally, the 

following must be considered during a biological data usability determination:

• Understanding the purpose for the bioassessment sampling, including specific 

project objectives, and determining the extent to which the bioassessment data 

set fulfills the objectives of the project or Program. The environmental 
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conditions associated with the sample (e.g., climatic, hydrologic, site location, 

habitat, etc.) must be consistent with the study objectives;

• Evaluating laboratory and field quality control measures and other supporting 

data, including the determination of the pattern, frequency, and magnitude of 

any quality control deficiencies associated with the results. This also may involve 

evaluating corroborative data (e.g., performance tests, data from other sampling 

entities);

• Determining the relationship between the bioassessment result, the associated 

decision or action level (e.g., water quality criteria), and the minimum detectable 

difference associated with the method; and

• Determining the reasonable cause for a poor bioassessment score (e.g., water 

quality, hydrology, and/or habitat) and ensuring that the data are appropriately 

used to address the causative factor(s). 

Determining the Extent to Which the Bioassessment Data Set Fulfills the 

Objectives of the Project

Designing a sampling strategy that focuses on answering specific environmental 

questions is critical in the bioassessment process, so that confounding variables may be 

controlled for to the degree possible. Data collected to evaluate one environmental 

stressor may not be suitable for determining the influence from other stressors. The 

Department shall examine the purpose of the data collection, the associated potential 

confounding variables, and ensure that the results are used in a manner consistent with 

the study objectives. 

Example: DEP scientists design a study to evaluate the effects of water withdrawls 

on the invertebrate community of a stream. SCIs were collected at typical water 

levels prior to the withdrawls to establish background SCI scores. Subsequent to

significant consumptive water use, SCIs were collected during extremely low water 

levels. Although the stream had high SCI scores prior to the consumptive water use, 

numerous SCI failures were noted after the water withdrawls. In this scenario, the SCI 

failures observed during the low water levels should not be included in Impaired 

Waters Rule (IWR) listing decisions, because these samples were collected during 

conditions inconsistent with the objectives of IWR studies. 

Evaluating Staff Capability, Quality Control Measures, and Other Supporting 

Data
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Data must be collected by qualified samplers, using the appropriate DEP Standard 

Operating Procedures (SOPs), following the concepts outlined in this SCI Primer. The SCI

must be performed by individuals that have passed the proficiency test described in DEP 

SOP SCI 1300. Samplers must conduct the assessment per DEP SOP SCI 1100, following 

other guidelines outlined in this Primer. SCI scores must be calculated in accordance 

with SOP SCI 2100.

Quality control information will be systematically evaluated and assessed against the 

objectives of the study before a usability decision will be made. For example, the 

purpose for which bioassessment data are collected can vary widely, and may include 

such diverse activities as: initial screening or scoping studies, assessing waters for IWR 

purposes, or determining whether a stream created as part of an Environmental 

Resource Permit mitigation project has been successful. A quality control failure that 

may be tolerated for a screening study would not be acceptable for IWR purposes or 

declaring the success or failure of a restoration project. 

As applicable to the data usability assessment process, any record associated with a 

reported sample result or set of sample results may be audited, per Chapter 62-160.240 

and 62-160.340, F.A.C. Both original (“raw”) and reduced or summarized versions of 

data records may be inspected to determine the acceptability of results, based on an 

evaluation the sample data and associated quality control records.

If any aspect of the assessment appears erroneous or suggests that the assessment was 

not made according to the SOPs (e.g., excessive family-level identifications, sampling 

conducted during extreme water levels not in accordance with the sampling objectives), 

the Department will further investigate the credibility of the bioassessment results. This 

may involve follow up audits of samplers or analysts and potential data rejection. 

Example: An SCI was conducted in a small stream in a National Forest as part of a 

probabilistic sampling network. Sampling was conducted during a drought year, and 

the stream’s water level was low enough that the majority of the habitat was 

exposed to air. Very few invertebrates were present in the sample (less than 150 

individuals, however, the lab failed to qualify the sample with “x”) and the stream

received a failing SCI score. When the results were considered for IWR listing 

purposes (Chapter 62-303, F.A.C.), data users examined the rainfall and hydrograph 

data from the area and determined, from these data and from site photos, that the 

severely low water level did not allow for a representative assessment of the 

stream’s invertebrate community. Further, the minimum required number of 

individual organisms (two aliquots of 150) were not identified in the laboratory (and 

the sample was not properly qualified with “x”). Therefore, these SCI results were 

not used for IWR listing purposes.

Example: A county conducts SCI sampling twice annually on a river of local interest. 

During the first three years of the program, the average SCI scores were 42, 55, and 
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48 (all passing scores). On the fourth year, a new consultant (including the sampling 

team and laboratory) conducted the SCIs, and the river received a failing score of 25. 

Upon investigation, data users noted that no one on the sampling team had passed 

the SCI proficiency test and that a high proportion of taxa identified in the laboratory 

were to the family level only (not to the level required by the SOP). Because the 

samplers did not demonstrate the required expertise and the laboratory SOPs were 

not properly followed, the year 4 SCI data were not considered usable, and DEP 

worked with the county to correct the deficiencies. 

Determining the Relationship Between the Bioassessment Result, the Water 

Quality Criterion, and the Minimum Detectable Difference Associated with the 

Method

As in all scientific measurements, there is a quantified level of uncertainty associated 

with bioassessment results, known as the Minimum Detectable Difference (MDD). 

When SCIs are compared along a longitudinal or temporal gradient, differences in scores 

greater than the MDD (plus or minus 13 points) are considered to be statistically 

reliable.

Example: Staff from the Florida Fish and Wildlife Conservation Commission Invasive 

Plant Management program conducted an herbicide treatment in a spring-fed river

to control the invasive exotic plant, Hydrilla verticillata. The average SCI score before 

control efforts was 24, and the average score nine months after control efforts was 

50 (an increase of 26 points). Because the difference in SCI scores was greater than 

the MDD (statistically reliable), the management actions were considered successful. 

Determining the Reasonable Cause for a Bioassessment Failure

Failure of the SCI indicates that the stream does not meet the Clean Water Act goal of 

biological integrity, as measured by community structure and function, but the reason 

for the unacceptable condition must still be explained. For IWR purposes, the pollutant 

causing the biological degradation must be identified prior to developing a TMDL. 

Although a stream could have a failing SCI due to water quality problems (e.g., toxic 

substances or excess nutrients), it is possible that habitat disruption, hydrologic

alterations, or other physical disturbances are significant stressors. If factors other than 

water quality are determined to be the cause of the SCI failure, DEP will address those 

factors through avenues other than the TMDL program.

Example: A stream fails the SCI, but data indicate the stream is not impaired for any 

water quality parameter. DEP biologists determine that the stream habitat 

assessment score was less than 80, and that the system had been artificially 

channelized in the 1960s. In this scenario, pollutant reduction is not required, but 
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physical restoration activities or reclassification of the waterbody would be 

potentially appropriate actions. 

Summary of SCI Data Usability

To determine appropriate actions associated with bioassessment results, DEP will 

review and evaluate the following information: 

• The purpose for collecting the bioassessment data and the degree to which the 

study fulfilled the objectives;

• The documented quality control measures and other supporting data, as well as 

the pattern, frequency, and magnitude of any quality control deficiencies 

associated with the results;

• The relationship between the results, the water quality criterion, and the 

Minimum Detectible Difference associated with the method; and

• A reasonable determination of the cause of the bioassessment failures.

From this evaluation, DEP will determine how the data can be used by the relevant 

Department programs. Biological health usability assessments will evaluate the above 

factors relative to DEP program or project objectives, and the follow the principles 

characterized in this guidance document to draw an “overall conclusion” concerning the 

usability of the data set consistent with the processes and examples provided in this 

document. 

7. SCI Training Materials, Training Requirements, and 

Checklists

See: http://www.dep.state.fl.us/water/bioassess/training.htm

8. Literature Cited

Brown, M. T., and B. Vivas. 2004. Landscape development intensity index. 

Environmental Monitoring and Assessment 101: 289-309

Fore, L.S, R.B. Frydenborg, D. Miller, T. Frick, D. Whiting, J. Espy, and L. Wolfe. 2007. 

Development and Testing of Biomonitoring Tools for Macroinvertebrates in 

Florida Streams. Florida Dept. Environmental Protection. 110 pp.