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Browse History: Methods (2011)

Chesapeake Bay - Methods


2011 methods for the aquatic grasses and the benthic community were affected by Hurricane Irene (August 27-28) and Tropical Storm Lee (September 7th).

Aquatic grasses: Parts of the Patuxent and Potomac Rivers were not mapped during the annual aquatic grasses survey in 2011. Therefore, the 2011 scores for the Patuxent and Potomac aquatic grasses are estimated by combining 2010 data, from those areas not mapped, with 2011 data for areas that were mapped. Due to the fact that aquatic grasses scores went down in 2011, we expect that using 2010 data for the Patuxent and Potomac overestimates the 2011 score.

Benthic community: Areas in the upper Bay that are usually low mesohaline, had tidal fresh bottom salinities after Lee. Data providers compared the species composition of some of the 2011 sites with the species composition of nearby sites sampled in 2010. The species composition was similar. However, because of habitat salinity class differences, the BIBI (Benthic Index of Biotic Integrity) was quite different when calculated on the lower salinity classes of 2011. Therefore, a salinity class correction was necessary for making the BIBI more comparable to previous years. Box plots of bottom salinity for all sites, 1995-2010 were made. Five years for which the salinity was clearly too high or too low (1995, 1996, 1999, 2002, and 2004) were removed. Using GIS, the bottom salinity values of the remaining years were mapped and superimposed the 2011 sites on the map. Then, the salinity class of the 2011 sites were re-assigned to reflect the predominant salinity class of the average year. Some of the 2011 sites did not need re-assignment because their salinity, although low (e.g., 6 ) was still within the salinity class of the average year (e.g., 5-12). Affected sites included many of the sites in the upper Bay and the upper Maryland western tributaries strata; some of the sites in the Maryland eastern tributaries and the Maryland main stem; and some of the sites in the Patuxent River. The salinity class of sites sampled prior to the storms were not evaluated or re-assigned. The 2011 sites in Virginia were all sampled prior to the storms so they did not need re-assignment nor did they exhibit lower salinity than expected.

General Methods

Ecosystem health report cards are an effective means of tracking and reporting the health of a waterway at both local and regional scales. A report card has being developed within the Chesapeake Bay science and management community in order to provide a transparent, timely, and geographically detailed annual assessment of Chesapeake Bay health.

Ecocheck methods newsletter

Calculating the Chesapeake Bay report card scores

This newsletter was produced for the inaugural report card in 2006, but the methods described are the same for all years. Click thumbnail to download.


Technical Methods Document

Development and evaluation of a spatially-explicit index of Chesapeake Bay health
Marine Pollution Bulletin 59(1-3): 14-25

This paper provides a more detailed of the methodology employed in generating the Bay Health Index.


Technical Methods Document

Supporting analysis for the report card scores

This document summarizes additional water quality analysis conducted for some reporting regions. This report was produced for the 2007 report card. Analysis was conducted for the Tidal Monitoring and Anlaysis workgroup by Jeni Keisman. Click thumbnail to download.



Chesapeake Bay health has been affected by elevated nutrient and sediment loads, resulting in water quality and biotic (biological) degradation. For the report card, Chesapeake Bay health is defined as the progress of six indicators towards established ecological thresholds. The three water quality indicators are chlorophyll a, dissolved oxygen, and water clarity, and the three biotic indicators are aquatic grasses (submerged aquatic vegetation), Benthic Index of Biotic Integrity (soft bottom only), and Phytoplankton Index of Biotic Integrity.

Conceptual Diagram Phytoplankton Index of Biotic Integrity icon Phytoplankton Index of Biotic Integrity icon Phytoplankton Index of Biotic Integrity icon Phytoplankton Index of Biotic Integrity icon Phytoplankton Index of Biotic Integrity icon Benthic Index of Biotic Integrity icon Benthic Index of Biotic Integrity icon Benthic Index of Biotic Integrity icon Benthic Index of Biotic Integrity icon Aquatic Grasses icon Aquatic Grasses icon Aquatic Grasses icon Aquatic Grasses icon Water Clarity icon Water Clarity icon Water Clarity icon Water Clarity icon Dissolved Oxygen icon Dissolved Oxygen icon Dissolved Oxygen icon Dissolved Oxygen icon Chlorophyll a icon Chlorophyll a icon Chlorophyll a icon Chlorophyll a icon Chlorophyll a icon

Indicators for the Chesapeake Bay Health Index were chosen so that they would relate to the management objectives established in the Chesapeake 2000 Agreement, represent key ecological processes, and fulfill practical requirements such as data availability and geographic coverage. The goal of improved Bay health through nutrient and sediment reductions should result in the indicators meeting established ecological thresholds. Threshold values were established for each indicator based on published scientific literature and technical reports. Measuring progress towards thresholds allows for both combining diverse indicators into indices and comparison between Bay regions. Monitoring data were assessed against the threshold values by determining the percentage of samples passing the thresholds over the period of interest. Aquatic grasses were assessed as the proportion of the restoration goal present. The Bay was divided into 15 reporting regions and the average of the three water quality indicators was used to generate the Water Quality Index, and the average of the three biotic indicators used to generate the Biotic Index. The Chesapeake Bay Health Index was determined by averaging the Water Quality and Biotic Index values for each reporting region.


Reporting Regions

Reporting Regions Map Lower Bay Upper Bay York River Elizabeth River James River Rappahannock River Lower Eastern Shore Mid Bay Potomac River Patuxent River Choptank River Upper Eastern Shore Lower Western Shore (MD) Patapsco-Back Rivers Upper Western Shore Mid Bay


Indicators, Thresholds and Indices

Report Card Methodology Chlorophyll a icon Dissolved Oxygen icon Water Clarity icon Aquatic Grasses icon Benthic Index of Biotic Integrity icon Phytoplankton Index of Biotic Integrity icon Bay Health Index icon Biotic Index icon Water Quality Index icon


Water quality and biotic indicators combined into indices

Water quality was measured at 144 sites, with a maximum of 11 times per period of interest. Spatial interpolations of average water quality conditions were produced to show spatial variability. The frequency that each water quality parameter exceeded established thresholds at each station was then calculated and mapped. For each sampling station, the frequency that each indicator exceeded the threshold was combined into a single score, the Water Quality Index (WQI), and then mapped. The Water Quality Index was calculated by averaging the area weighted scores for water clarity, dissolved oxygen, and chlorophyll a for each reporting region.

The distribution of aquatic grasses is estimated each year using aerial surveys. The area (hectares) of aquatic grasses relative to the restoration goal is calculated for each reporting region. Samples for assessing benthic community were collected at approximately 250 sites over the spring and summer. The area of the reporting region exceeding the Index of Biotic Integrity (IBI) threshold was calculated. Samples for assessing the phytoplankton community were collected at approximately 31 stations, up to 6 times during spring and summer. The frequency that the Phytoplankton Index of Biotic Integrity score exceeded the threshold was calculated for each reporting region. The Biotic Index was calculated by averaging the area weighted scores for aquatic grass, Benthic IBI, and Phytoplankton IBI for each reporting region.

The Bay Health Index (BHI) was calculated by averaging the Water Quality Index and Biotic Index scores for each reporting region.

Methods Diagram Phytoplankton Index of Biotic Integrity icon Benthic Index of Biotic Integrity icon Aquatic Grasses icon Water Clarity icon Dissolved Oxygen icon Chlorophyll a icon Biotic Index icon Water Quality Index icon Bay Health Index icon

Testing the sensitivity of the Water Quality Index

The Water Quality Index (WQI) needs to be sensitive to changes in the amount of nutrients delivered to the Bay so that future changes in management actions can be detected. To do this, the Index was tested by comparing a low flow/low nutrient year (2002) with a high flow/high nutrient year (2003). The year 2002 approximated the 175 and 12.8 million pound restoration goals for nitrogen and phosphorus loads, respectively, to the Bay. 2003 is approximately >2.5x and >8x these restoration goals. The methods and thresholds used to calculate WQI scores proved to be sensitive to nutrients. For example, the 2002 score was substantially higher than the 2003 score for the Choptank, James, and Mid Bay regions. However, some regions did not show distinct differences between the two years (e.g., Patapsco and Back, and York Rivers), perhaps illustrating that factors other than flow and nutrients play a larger role in the health of these systems.

WQI Comparison Graph


Comparing Health Reports

The Chesapeake Bay report card is unique in that it provides a geographically detailed and integrated approach to form numerical rankings of 15 reporting regions on an annual basis. This approach compliments those focusing on Bay-wide assessment over longer time frames. The geographic detail provided in the report card reflects the complexity of Chesapeake Bay and its tributaries, and provides information that can help guide and focus restoration efforts. The report card is a developing product, with a more complete assessment of Bay health expected in the future. Future report cards will aim to include indicators of fish and shellfish status at suitable spatial scales and time frames.

Report Card Cover

Chesapeake Bay Report Card

  • Bay and tributary specific assessment using six indicators
  • Integrated into an index
  • Provides full assessment since 2006 and trends since 1986
  • Numerical rankings of reporting regions
  • Continued development and refinement required

CBP Report Cardpdf icon

Chesapeake Bay health and restoration assessment

  • Bay-wide assessment using 13 indicators
  • Provides assessment for the past 20 years
  • Numerical ranking of Bay-wide indicators
  • Continued development and refinement required