An official website of the United States government.

This is not the current EPA website. To navigate to the current EPA website, please go to This website is historical material reflecting the EPA website as it existed on January 19, 2021. This website is no longer updated and links to external websites and some internal pages may not work. More information »

National Estuary Program (NEP)

How the National Estuary Programs Address Toxics

If consumed by humans, organisms exposed to certain toxics can pose a risk to human health. Wildlife and aquatic plants and animals can be harmed by consuming contaminated fish and water.

The following are common toxics that threaten estuaries:

  • Metals, such as mercury
  • Polycyclic aromatic hydrocarbons (PAHs)
  • Polychlorinated biphenyls (PCBs)
  • Pesticides

Ways that such toxics can enter waterways include:

  • Storm drains
  • Industrial discharges
  • Runoff from lawns, streets and farmlands
  • Discharges from sewage treatment plants
  • Atmospheric deposition

NEP Approach/Success Stories

On this page:

New York-New Jersey Harbor & Estuary Program

In 2001, the Harbor & Estuary Program’s Toxics Work Group initiated a polychlorinated biphenyls (PCBs) monitoring project in partnership with the Linden Roselle Sewage Authority. In 2012, water quality managers identified a significant source of PCBs and remediated the site polluted by those toxic compounds.

Top of Page

San Juan Bay Estuary Program (SJBEP)

San Juan Bay Estuary Program (located in Puerto Rico) conducted a toxics recovery project Condado Lagoon, which had become a giant cesspool due to high concentrations of fecal coliform. Here, SJBEP worked with partners to eradicate the sewage discharge and improve water quality.

In 2009, the last large-scale infrastructure work done in the area eliminated a sanitary water pump station with a long history of sewage bypass.

Top of Page

San Francisco Estuary Partnership (SFEP)

Outdoor insecticide applications—commonly used in California to control ants—have been directly linked to toxicity in California creeks. In 1998, all urban creeks in the San Francisco Bay Area were added to the Clean Water Act Section 303(d) list due to known or suspected impairment from the pesticide diazinon. Since 2004, diazinon is no longer available for purchase, and applicators are using other pesticides such as pyrethroids instead.

Indoor pesticide applications also are linked to water pollution due to clean up and application methods. That is, when pesticides wash down drains, they pass through water treatment plants that are not designed to remove these substances and can reach water bodies.

The SFEP's Urban Pesticide Pollution Prevention (UP3) Project works to prevent water pollution from urban pesticide use. The UP3 Project tracks, analyzes and shares information about:

  1. Urban pesticide use.
  2. Regulatory processes related to pesticides of concern.
  3. Science and monitoring data on pesticides.

The UP3 Project supports the Urban Pesticides Committee, which for more than a decade has provided a forum for stakeholders to coordinate and develop ways to reduce pesticide impacts on aquatic life. The UP3 Project also provides tools to help municipalities reduce their pesticide use. This Project works to reduce this toxicity in creeks in three main ways:

  • Providing tools to municipalities to reduce municipal pesticide use and to conduct outreach to their communities on less-toxic methods of pest control (e.g., baits, caulking and improved sanitation);
  • Compiling the latest relevant scientific information and providing regular e-mail updates and informative annual reports;
  • Providing technical assistance to California Water Boards and municipalities to promote the U.S. Environmental Protection Agency (U.S. EPA) and the California Department of Pesticide Regulation (DPR) support for preventing water quality problems from pesticides.

Specifically, the SFEP UP3 has:

  • Established the UP3 website, which is cited by researchers, water quality managers and regulators as a key resource for their work;
  • Trained hundreds of municipal staff and pest managers on the links between pesticide use and water quality and how to manage ant problems using integrated pest management;
  • Completed the only available analysis of urban pesticide use patterns (PDF)(14 pp, 231 K, About PDF) Exitto inform water quality and pesticide agency responses to pesticide-related surface water toxicity.

For more information, see: Urban Pesticide Pollution Prevention (UP3) Project Exit

Additionally, the SFEP collaborated with the San Francisco Estuary Institute (SFEI) to conduct annual water quality monitoring and water quality trends analysis in the San Francisco Bay. These partners develop protocols for surface water quality monitoring, such as its toxicity identification evaluation (TIE) procedures for pyrethroid-caused toxicity that are now routinely used in toxicity testing laboratories throughout California.

Top of Page