The short version
In 1993 the US Environmental Protection Agency chose Waquoit Bay as one of five watersheds to test a new way of weighing all the threats to a whole watershed at once. This 1996 draft report is the first stage of that work. A volunteer team led by the Waquoit Bay National Estuarine Research Reserve and EPA’s New England office asked the public what they valued about the bay, agreed on a goal with local, state and federal agencies, and mapped how human activities could be causing harm. When the team ranked seven possible threats, nutrients came out first. That ranking is why the final 2002 assessment zeroed in on nitrogen and eelgrass.
What the report covers
EPA’s risk assessment process starts with planning (agreeing on goals and scope) and problem formulation (deciding what to measure and how harm might happen). This report covers those two steps; the analysis came later.
- EPA and the Reserve held a public forum on September 21, 1993, asking two questions: what do you value in the watershed, and what is putting it at risk?
- The team gathered the written goals of organizations with a stake in the bay, from the Cape Cod Commission and state environmental agency to local groups, including Citizens for the Protection of Waquoit Bay.
- At a meeting on February 24, 1995, representatives of those organizations approved a management goal and ten more specific objectives.
- The team picked eight things to measure (“assessment endpoints”), such as eelgrass extent, fish and shellfish, herring and trout runs, pond health, and contamination of seafood. It then drew diagrams linking human activities to stressors and to those endpoints, and ranked the stressors using structured expert judgment.
What they found
- A shared goal. Participants agreed the aim should be to restore and maintain water quality and habitat in the bay, its rivers, ponds and wetlands, so that it supports diverse, self-sustaining fish and shellfish, and to reverse the ongoing decline.
- The bay was already in trouble. The report describes eelgrass as almost gone from the bay, bay scallops as having virtually disappeared, and mass die-offs of fish and shellfish after runs of cloudy summer days.
- Seven stressors. The team listed nutrients; toxic chemicals (including groundwater plumes from the Massachusetts Military Reservation); suspended sediments; physical damage to habitat from docks, moorings, propellers and clamming; altered stream flow; fishing pressure; and eelgrass wasting disease.
- Nutrients ranked first. In every version of the ranking, nutrients came first and physical habitat damage second, with sediments and disease last. The team concluded that
excess nutrient loading is the principal stressor
(U.S. EPA, 1996), but stressed the ranking was preliminary and not yet reviewed by outside experts. - Nitrogen in the pipeline. Citing earlier work by Sham and colleagues, the report noted that the load then reaching the bay was about 70 percent of what existing homes and buildings would eventually deliver through groundwater.
- A plan to put numbers on it. The next step would be a regional model linking nitrogen loads to eelgrass cover, using roughly 50 of the 90 or so semi-enclosed estuaries along the south Cape and the islands, plus forecasts of future loads as the watershed built out.
- Done on a shoestring. No new data were collected. Team members gave their time without grant or contract funding.
What it means for Waquoit Bay today
This draft is where the official focus on nitrogen began. Residents, agencies and local groups, CPWB among them, helped set the goal, and the team’s ranking pointed the follow-up work at nitrogen and eelgrass. That follow-up became EPA’s final 2002 risk assessment, which put numbers on the link between nitrogen loads and eelgrass loss (see our summary of the 2002 risk assessment).
The report’s point about nitrogen already in the groundwater still matters: even after sources are cut, the bay keeps receiving older nitrogen for years. Later modeling has looked again at how long that groundwater pipeline is (see our summary of EPA’s legacy nitrogen model). Note that this is a 1996 draft, and some of its details were revised in later work.
Read the report
U.S. Environmental Protection Agency, Risk Assessment Forum. (1996). Waquoit Bay watershed: Ecological risk assessment planning and problem formulation (Draft, June 13, 1996; EPA/630/R-96/004A). Washington, DC. https://nepis.epa.gov/Exe/ZyPURL.cgi?Dockey=30004YEL.TXT
License: This is a US federal government report and is in the public domain. The PDF below is the scanned copy from EPA’s National Service Center for Environmental Publications, reproduced unmodified. It is marked as a draft; we could not find a later final version of this planning document online, and the work was completed in EPA’s 2002 risk assessment. The card image is the report’s first page (public domain, US Government work).
Drafted with AI assistance from the linked source.


