Monitoring Program Design

Chemical measures refer to the chemical composition of the water and can be attributed to natural and human sources. Some examples of chemical substances in the water are nutrients (e.g., phosphorus and nitrogen), heavy metals (e.g., lead and mercury), acidity, hardness, salts (e.g., sodium and chloride), and contaminants of emerging concern (e.g., PFAS and PFOA).

Physical measures cover attributes that are measured within the water and the surrounding watershed. Some examples of physical measures within the water include temperature, dissolved oxygen, turbidity, total dissolved solids, salinity, depth, and substrate and habitat summaries. It is often informative to understand the non-aquatic physical measures in the immediate area and the watershed, which can impact water quality. Some examples include the amount of vegetation on the shore or bank of a waterbody, the amount of canopy cover above a waterbody, land use (e.g., forested, agricultural, residential, industrial, etc.) in the watershed, elevation, and geology.

Biomonitoring and Biological Assessment Profile (BAP) Scores

For Water Quality Evaluation

Biomonitoring

Biological monitoring, or biomonitoring, provides information on the relative health of an ecosystem. The organisms found in our waterbodies are good indicators of water quality because they must survive in the conditions prior to our monitoring. The types and numbers of organisms collected from polluted water differ from those collected in unpolluted water. These organisms help us determine the quality of the 

water and detect changes over time. Macroinvertebrates, fish, and algae are all widely used in biomonitoring. Although DEC collects information on all these aquatic organisms, macroinvertebrates are collected and analyzed most routinely. Macroinvertebrates provide accurate means of water quality evaluation because of their diversity and abundance, inability to avoid discharges or other stressors, and their community level sensitivity to environmental stressors.

BAP Score Overview

The macroinvertebrate community condition is characterized using a multi-metric index of water quality called the Biological Assessment Profile (BAP) score. The BAP averages individual metrics converted to a common 10 scale and assigns levels of macroinvertebrate impact to ranges of BAP score (0.00–2.49 severely impacted, 2.50–4.99 moderately impacted, 5.00–7.49 slightly impacted, and 7.50–10.00 non-impacted). BAP scores below 5.00 are associated with significant loss of biodiversity, functional organization, and ability to support a balanced community as compared to natural conditions and suggests that water quality does not support the propagation and survival of aquatic life. The goal of this document is to provide an overview of the different aspects of BAP scores, including collection methods, individual identification, scoring, and applications.

Field Sampling

Macroinvertebrate collection methods differ based on the type of habitat and current flow conditions of the specific stream. The primary methods of field sampling are the traveling kick-net, low gradient multi-habitat, and multiplate sampling, as well as a composite kick method designed for lakes sampling. Each method has been developed and calibrated to provide a representative picture of the biological condition for that waterbody and habitat. For a more detailed explanation of sampling methods and site selection, please see SOP-AMB-208.

Traveling Kick-Net: This method works in shallow, flowing streams where you can wade safely. Scientists focus on fast-flowing sections with rocks and small stones known as riffles. A small net is held downstream, while the sampler gently kicks and stirs the stream bottom to dislodge organisms into the net. The sample is collected over 5 minutes and 5 meters along a diagonal path across the stream to capture a variety of microhabitats. A demonstration of the traveling kick-net can be seen in figure 1.

Low Gradient Multi-Habitat: This method is used in slow-moving, wadeable streams where the bottom is soft—made of silt, clay, or sand—and riffles are rare or absent. This approach captures organisms from a variety of habitats typical of low-gradient streams. Eight points across four habitat types are sampled in this method. At each point, a net is used to perform a 30-second “jab and sweep” method to dislodge organisms. All eight sampling points are then combined and processed as one composite sample. An example of a low-gradient site can be seen in figure 2.

Multiplate: The multiplate sampler is an artificial substrate method used to monitor water quality in deeper or non-wadeable rivers where traditional kick sampling is not possible. A device made of three square hardboard plates mounted on a turnbuckle is deployed in the stream for five weeks. The sampler provides a standardized surface for aquatic insects and other macroinvertebrates to colonize. An image of a multiplate can be seen in figure 3. Multiplates have been used by New York State scientists to collect water quality data in non-wadeable streams for over 50 years, dating back to the early 1970s.

Lake Shoreline Sampling: Scientists select eight evenly spaced locations around the main shoreline of each lake, starting from a randomly chosen point. Samples are collected at a depth of 1 meter, about 5–10 meters from shore. A kick-net is used to sample a 1x1 meter area. The bottom is disturbed for 1 minute to dislodge organisms into the net. The eight sampling points are combined and processed as one composite sample. An example of lake shoreline sampling can be seen in figure 4.

Individual Identification

All samples are preserved in ethanol in field. After returning from the field, samples are sorted to subsample targets according to method and identified to the highest taxonomic resolution possible, often genus or species. For more detailed information on sample processing and macroinvertebrate identifications, please see SOP-AMB-214.

Calculating BAP Scores

BAP is a method of evaluating biological community condition on a common scale of water quality impact. Individual metrics from those methods described previously are converted to a common 10-scale based on a series of equations. The combination of metrics, which differ based on the type of sample collected and the habitat from which the sample was taken, is what is used to form the BAP score. This score correlates to an impact category for each site. The evaluation of surface water quality uses a four-tiered system of impact categorization based on the macroinvertebrate community. 

The four tiers are:

1. Non-Impact (7.50 – 10.00), 
2. Slight Impact (5.00 – 7.49), 
3. Moderate Impact (2.50 – 4.99), and 
4. Severe Impact (0.00 - 2.49).

BAP scores below 5.00 (moderately or severely impacted) indicates changes in aquatic life associated with significant loss of biodiversity, change in functional organization, and an inability to support a balanced community of aquatic life compared to natural conditions. The adjacent figure illustrates that as stressor levels increase, BAP scores decrease.

Various combinations of individual metrics are used to calculate the BAP score and are dependent upon the type of habitat. For streams and rivers, these metrics include species richness, EPT richness, Hilsenhoff’s biotic index, percent model affinity, nutrient biotic index, species diversity, and non-Chironomidae and Oligochaeta richness. For lakes, ponds and reservoirs, these metrics include Chironomid taxa richness, Shannon diversity of COTE (Coleoptera, Odonata, Trichoptera, and Ephemeroptera) taxa, percent richness insect taxa, percent intolerant taxa, and the richness of clinger and sprawler taxa. Metrics are selected to represent different aspects of community structure and function and the specific metric combinations used to calculate the BAP differ depending on the sampling method used. For more information about how BAP scores are calculated, please see SOP-AMB-216.

Applications

The New York State Department of Environmental Conservation (DEC) utilizes BAP scores in a variety of ways for both waterbody management and scientific research. Listed below are some examples of how BAP scores are applied at the DEC.

1. Because the macroinvertebrate community is sensitive to a wide range of stressors, BAP scores act as a screening tool for environmental managers to identify at-risk waterbodies and prioritize restoration efforts. 
2. Within the Consolidated Assessment and Listing Methodology (CALM) framework, BAP scores are used as supplemental indicators that provide a biological context that compliments chemical and physical data. 
3. BAP scores are used to evaluate the impact of disturbances such as permitted discharges, where changes in macroinvertebrate community structure can indicate biological impairment when chemical parameters appear within acceptable ranges, or are currently unavailable. They can also be used to confirm that a chemical impairment is negatively affecting the biological community of an aquatic system.

DEC has been collecting macroinvertebrate communities and calculating BAP scores across the state since the 1970s, culminating into a long-term dataset. This 40-Year trend analysis uses this dataset to illustrate the role of BAP scores in tracking ecological recovery and degradation over time.

Conclusions

Overall, BAP scores offer a straightforward and robust way to understand water quality. It works well with different habitat types and flow regimes, and combines multiple biological measures into a simple score that reflects water quality conditions. This score turns a complex biological community response into an easy to understand value that simplifies communication about water quality between scientists, the public, engineers, and decision makers. 

Glossary

• Biological Assessment Profile (BAP): a multimetric index of biological integrity used in NYS to translate macroinvertebrate community data into numerical water quality score between 0 (poor) and 10 (very high).
• Hilsenhoff’s Biotic Index: A measure of the condition of a biological community representing the degree of environmental disturbance on that community. Biotic indices are often used to determine the impact of water pollution on aquatic life based on various characteristics of the community present.
• Community: Group of populations of organisms interacting in a habitat
• Discharge: Stream and river discharge is a measure of the volume of water passing a specific location over a specified unit of time. Discharge is therefore the product of stream velocity times stream depth times stream width.
• EPT Richness: Number of taxa of mayflies (Ephemeroptera), stoneflies (Plecoptera), and caddisflies (Trichoptera) in a sample or subsample Impact: Change in the physical, chemical or biological condition of a waterbody.
• Impairment: Detrimental effect caused by an impact.
• Index (pl. ‘indices’): Number, metric or parameter derived from sample data used as a measure of water quality.
• Macroinvertebrate: Larger-than-microscopic invertebrate animal that lives at least part of its life in aquatic habitats.
• Metric: an attribute of a biological community that is sensitive to changes in water quality.
• Non-Chironomidae and Oligochaeta: number of taxa in the sample excluding those in the Chironomidae family and Oligochaeta subclass.
• Nutrient Biotic Index: A measure of the macroinvertebrate community response to phosphorus developed specifically for use in NYS streams and rivers.
• Organism: Living individual.
• Percent Model Affinity: Is a measure of similarity to a model non-impacted benthic macroinvertebrate community based on percent abundance in 7 major groups. This measure is described in detail in Novak, M.A. and R.W. Bode. 1992. Percent model affinity, a new measure of macroinvertebrate community composition. J. North American Benthological Society 11(1):80-85.
• Riffle: Wadeable stretch of stream, usually with a rubble bottom and sufficient current to break the water surface by the flow; rapids.
• Species richness: Number of macroinvertebrate taxa in a sample or subsample.
• Species Diversity: Shannon diversity index, a metric accounting for both abundance and evenness of species present.
• Tolerant: Ability to survive poor water quality.

The Water Quality Measures by Program table is a high-level overview of the chemical, physical, and biological measures collected by DEC's Division of Water monitoring programs. Programs that are not managed by the Division of Water, such as the Great Lakes, Wetland, and Coastal programs, are not incorporated into the table below. For a more detailed overview of the measures collected by the Division of Water, please refer to the related Quality Assurance Project Plans (QAPPs) found on the DEC's Quality assurance webpage.

Following the RIBS cycle, the Screening Network provides an assessment of water quality at sampling sites statewide based on chemical, biological, and physical monitoring. Data are collected from up to 15 lakes and approximately ~60 river and stream locations in each major drainage basin.

Please see the Water Quality Measures by Program table for an overview of the water quality measures collected by this program.

Special Studies are designed to answer specific questions regarding habitat and water quality. These studies often employ sampling such as depth integrated water chemistry, bottom sediment and invertebrate tissue chemistry, toxicity testing, or habitat assessment, depending on the focus of the survey. Special studies are conducted in streams and lakes and typically span 1-2 years. Clean Water Planning and SPDES Permitting and Compliance monitoring are two common types of special studies.

Clean Water Planning Monitoring

DEC’s Integrated Report under CWA Section 305(b) and 303(d) describe the quality of all water resources in NYS and those specific waters that do not meet water quality standards, do not support best uses, and required the development of a TMDL, respectively. While the 303(d) list identifies waters that do not meet NYS’s water quality standards and do not support best uses, DEC uses an adaptive strategy for protection and restoration and prioritizing development of clean water plans across the state. Those priorities are described in the “Vision Approach” document available at Clean Water Plans – DEC.

The “Vision Approach” document is a prioritization framework based on EPA’s guidance in their 2022-2032 Vision for the Clean Water Act Section 303(d) Program. For those waterbody segments indicated as high priority, DEC may have additional water quality data collection needs associated with establishing a clean water plan. Data needs are determined on an annual basis according to the 303(d) program commitments made by the DEC to the EPA.

Data collected through DEC’s monitoring programs are used in the development of clean water plans. Data uses include:

• Consolidated Assessment and Listing Methodology (CALM);
• Vision waterbody prioritization;
• Watershed and waterbody modeling;
• Post clean water planning monitoring.

SPDES Permitting and Compliance Monitoring

DEC monitoring programs focus on ambient water quality. The programs do not collect water quality data from or near known discharges. Monitoring related to SPDES permitting and compliance is conducted at the specified outfall location in the permit, which consists of 100% treated wastewater. However, where appropriate, NYS allows acute and chronic mixing zones to be established of varying shapes and sizes based on the site-specific mixing characteristics. These are areas in the receiving water where impacts to aquatic life are allowed, but where acute (survival) and chronic (propagation) criteria must be met at the respective edges. For more information about SPDES permitting please visit: Wastewater, Stormwater and Water Withdrawal Permits.

Source Water Monitoring

DEC monitors ambient water quality of public water supplies (PWS) that are surface waters in support of the Drinking Water Source Protection Program (DWSP2), which is a locally led, state-supported program that empowers municipalities to improve and protect their public water sources. As part of this effort, DEC is working towards sampling all active and backup PWS to gain a better understanding of statewide ambient conditions and to prioritize future monitoring and outreach. 

Monitoring ambient water quality of PWS can proactively identify water quality concerns early and inform clean water planning to protect source waters. For municipalities interested in establishing PWS monitoring programs visit Recommendations for Monitoring Source Water Quality (PDF).

The Groundwater Ambient Monitoring Program is a collaborative effort between the DEC and the United State Geological Survey (USGS) to conduct yearly comprehensive sampling and analysis of groundwater including field and physical parameters, bacteria, nutrients, inorganics, organics (including pesticides and VOCs), and radiochemicals. Sampling is conducted by USGS using both public and private wells.

Sampling results are available through the National Weather System and data reports are available for each major basin through USGS’s Groundwater Quality Monitoring in NY webpage.

Beginning in 2024, DEC and USGS initiated a redesign effort of the monitoring program to ensure that it is efficiently and effectively addressing the evolving groundwater quality needs of the state. The redesign will include a thorough review of trends and drivers of groundwater water quality across the state to identify monitoring priorities and to improve the overall understanding of groundwater quality in the state. Future groundwater sampling will follow the redesigned program strategy. 

The Division of Water’s citizen science programs engage the public in water quality monitoring and management for our ponded and flowing waters. Other terms include participatory science, community science, or public participation in scientific research. 

Water Assessments by Volunteer Evaluators (WAVE)

WAVE is a citizen-based water quality assessment developed by DEC. The purpose of WAVE is to enable citizen and community scientists to collect biological data for assessment of water quality in wadeable streams in NYS. WAVE citizen and community scientists collect benthic macroinvertebrates any time between July 1 and September 30. Participants collect riffle-dwelling benthic macroinvertebrates and preserve one or two example specimens of each macroinvertebrate type in a voucher collection. See the 2022 publication NYS’s WAVE Method - Evaluation of a Method for Water Quality Monitoring by Citizen Scientists using Benthic Macroinvertebrates - PMC (nih.gov).

The WAVE program collects biological data at various locations around the state and provides the River and Stream Screening Network with potential future sites.

County, municipal, and not-for-profit organizations may use WAVE data to support local stream restoration and/or protection efforts. DEC is very interested in tracking these applications of the WAVE data. If you are involved or are aware of a use of the WAVE data, please contact the WAVE Coordinator.

The WAVE coordinator identifies all macroinvertebrates in the WAVE samples to the level of family and uses this data to calculate a WAVE score:

Become a WAVE Volunteer Today

To become a WAVE volunteer, you must first complete a participation waiver. Links to the WAVE waiver, survey forms and FAQs can be found in the Sampling Guide (PDF). 

WAVE training is available online. Get trained in the WAVE method today from the comfort of your own home using the WAVE Training video.

All WAVE announcements are sent to our DEC Delivers email list. To sign-up, visit DEC's email service webpage.

Citizens Statewide Lake Assessment Program (CSLAP)

The Citizens Statewide Lake Assessment Program (CSLAP) is a volunteer lake monitoring program directed by DEC staff in collaboration with the NYS Federation of Lake Associations (NYSFOLA). Through this program, relationships between lake associations, academic and private research institutions, and municipal, county, and state entities are built statewide. The program aims to collect representative water quality data in lakes throughout NYS to evaluate current and long-term water quality conditions, empower stakeholders to understand and protect water quality locally, and inform statewide waterbody management through assessment and listing and clean water planning.

Please see the Water Quality Measures by Program table for an overview of the water quality measures collected by this program. 

For more information, please visit: CSLAP Sampling Activities.

The DEC’s Shellfish Harvest Area Classification Unit monitors water quality in New York State’s marine district to classify waters for the harvest of shellfish. It uses the Systematic Random Sampling (SRS) strategy to monitor and assess approximately 1,500 sampling stations for fecal coliform bacteria levels. Testing results are assessed and compared to standards for the geomean and the 90th percentile to determine if the SRS analysis criteria is met to allow the harvest of shellfish. Analysis criteria can be found in the National Shellfish Sanitation Program’s Model Ordinance (NSSP-MO). 

The DEC’s Shellfisheries Bureau manages the Marine Biotoxin Monitoring Program to monitor marine habitats and to identify local waters where biotoxins may be occurring. Marine biotoxins have the potential to harm marine organisms and human health. 

For general information about shellfishing and temporary closures in New York State, please visit DEC’s Shellfishing webpage.

The DEC’s Great Lakes Watershed Program provides support to state and federal agencies, universities, nonprofit organizations, and local communities to protect and restore water quality in the Great Lakes. The program provides grant funding, coordinates training and educational opportunities, and foster’s community engagement and stewardship. For more information, please visit: Great Lakes - NYSDEC.

The DEC’s Division of Fish and Wildlife and the New York Natural Heritage Program monitor, assess, and regulate wetlands in NYS. Classification of all natural ecological community types in New York State, including wetland types, are available in an interactive map on DEC’s Environmental Resource Mapper and can be downloaded from the NYS GIS Clearinghouse. Wetland conditions are assessed through wetland rapid condition assessment methodology, known as NYRAM, a wetland functional assessment methodology, and participation in USEPA’s National Wetland Condition Assessment. Regulatory preservation, protection, and conservation are provided by the Freshwater Wetlands Program and the Tidal Wetlands Program. 

NYS has more than 80,000 freshwater river and stream miles. DEC’s River and Stream Probability Sampling collects and evaluates water quality in these waterbodies statewide on a 2-year cycle. Results from this effort provide statewide water quality condition estimates and are summarized in the 305(b) report.

DEC uses the GRTS algorithm for collecting a balanced set of stream sizes (Strahler Order) statewide. Without this algorithm, random sampling would be biased to smaller streams because they occur more frequently throughout the state. 

DEC adheres to the procedures outlined in the Rotating Integrated Basin Studies (RIBS) River and Streams Quality Assurance Project Plan to ensure uniformity of methods and data accuracy. These documents are available from DEC Water Quality Assurance webpage.

Please see the Water Quality Measures by Program table for an overview of the water quality measures collected by this program.

NYS has more than 7,600 freshwater lakes, ponds, and reservoirs that are used for recreation and supply water to homes, industries, and farms. DEC’s Lake Probability Sampling collects water quality samples and evaluates these waterbodies statewide on a 2-year cycle through the Lake Classification and Inventory (LCI) program. Results from this effort provide statewide water quality condition estimates and are summarized in the 305(b) report. 

LCI uses the GRTS algorithm for collecting a balanced set of lake sizes across the state. Without this algorithm random sampling would be biased to smaller lakes because they occur more frequently throughout the state.

DEC adheres to the procedures outlined in the LCI Lake Monitoring Program Quality Assurance Program Plan to ensure uniformity of methods and data accuracy. These documents are available from DEC Water Quality Assurance webpage.

Please see the Water Quality Measures by Program table for an overview of the water quality measures collected by this program.

The network of "routine" sites provides annual, statewide information for a network of permanent sites to understand long-term trends in flowing waters. Currently, there are 40 Routine Network sites across NYS, which are monitored annually regardless of the RIBS Monitoring cycle. Ambient water column chemistry is the primary focus of the Routine River Network and is collected 4 times each year. Sampling for the Routine River Network is largely conducted by DEC staff working in regional suboffices. Routine River Network sites are co-located with United States Geological Survey (USGS) gage stations to facilitate loading calculations for TMDL development and other watershed planning initiatives.

Data collection from these sites paired with other river and stream monitoring data, such as resident macroinvertebrate communities, have been instrumental in identifying statewide water quality trends over time. See DEC’s 2018 publication "Long-term trends in biological indicators and water quality in river and streams of NYS (1972 - 2012): Water Quality Trends in NYS"

Please see the Water Quality Measures by Program table for an overview of the water quality measures collected by this program. 

In collaboration with the USEPA and other Northeast States, DEC participates in Regional Monitoring Networks (RMNs) for Lakes and Streams. These RMNs collect biological, thermal, chemical, and hydrologic data from freshwater lakes, ponds, and wadeable streams. This information is used to help quantify and detect long-term changes in conditions of high-quality waterbodies. Detection of such changes can inform water quality criteria and indicator development, as well as responses to climate change impacts.

The Lake Routine Network captures long term trends and includes 28 sites sampled annually by a combination of CSLAP volunteers and DEC staff. Data and analysis of long-term trends in lakes help understand changes in water quality over time.