Nonpoint Source Pollution

Nonpoint source pollution (NPS) happens when water from rainfall, snowmelt or irrigation runs over land or through the ground and picks up pollutants and deposits them into rivers, streams, lakes, wetlands, or groundwater – and it’s a really big deal for water quality in Missouri. Pollution from nonpoint sources – storm sewers, failing septic systems, and underground storage tanks, and runoff from construction sites, mining areas, crop fields, pastures and confined animal feeding operations, and paved surfaces, rooftops and lawns — contribute huge quantities of bacteria, sediment, nitrate and phosphorus, chloride and other pollutants to our surface waters and groundwater. Atmospheric deposition and hydrologic modification are also sources of nonpoint source pollution.

Nonpoint source pollution is the greatest threat to the state’s waters. NPS was responsible for 87% of rivers and streams and 59% of lakes on Missouri’s 2020 303(d) list of impaired waters. 

In Missouri, significant sources of NPS pollution include agricultural land use, urban areas and abandoned mines. Using land management practices that reduce and slow runoff greatly reduces nonpoint source pollution. Reduction of NPS generally takes voluntary action. Learn more about NPS impacts, and ways to address them, by reviewing the Watersheds - PUB0243 fact sheet.

The department takes two general approaches to managing NPS pollution, one that relies on voluntary action through two programs that offer monetary incentives and grants, and another that is regulation-focused.

Nonpoint Source Management Program 

This program engages citizen organizations, federal, state and local governments, as well as universities and other stakeholders to plan for and implement NPS control practices and monitor for improvements to water quality. Project funding is provided by the U.S. Environmental Protection Agency though Section 319(h) of the federal Clean Water Act, with the department awarding subgrants that support 60% of total project costs. Section 319 subgrant projects target restoration and protection of waters impaired or threatened by NPS. The NPS Management Program is also a partner of the Natural Resources Conservation Service’s Mississippi River Basin Initiative (MRBI) and National Water Quality Initiative (NWQI). For more information about the department’s Nonpoint Source Management Program and Section 319 grant funding, visit the Nonpoint Source Pollution – Section 319 webpage.

Regulated Activities Related to NPS

While most nonpoint sources of pollution are not formally regulated, there are some activities that require a permit from the department. Permits are issued to control stormwater runoff from land disturbance activities of an acre or more, as well as for certain industries like biodiesel manufacturers, agrichemical producers and Concentrated Animal Feeding Operations (CAFOs). Other activities requiring a permit include clay, rock and mineral mining, abandoned mine land reclamation, land application of human and animal wastewater and underground petroleum storage. Construction, placement, dredging and filling, or general earth moving within a wetland or waterbody requires a 401 certification from the department and 404 permit from the U.S. Army Corps of Engineers. Single family septic systems, which can be nonpoint sources of pollution, fall under the jurisdiction and responsibility of the Missouri Department of Health and Senior Services.