Water Protection Program fact sheet
Division of Environmental Quality Director: Kyra Moore

This guidance document provides general program information, priorities, funding restrictions, definitions of basic terminology and answers to frequently asked questions related to the distribution of Section 319 grant funds on urban land. Urban land is defined as land that is currently not cropland, pastureland, rangeland, native pasture land, other land used to support livestock production or tree farms. The policies and guidance within this document primarily apply to urban projects. If you have any questions about circumstances under which this document applies, contact the Missouri Department of Natural Resources’ Financial Assistance Center at 573-751-1192 or MoDNR.NPSprogram@dnr.mo.gov.

Under Section 319 of the Clean Water Act, the Missouri Department of Natural Resources (department) provides federal grant funding for a wide variety of activities that work to reduce nonpoint source water pollution, including technical assistance, financial assistance, education, training, technology transfer, implementation and monitoring to assess the success of specific projects.

To be eligible to receive Section 319 grant funds to implement Best Management Practices (BMPs), Missouri’s Nonpoint   Source Program requires that a nine-element watershed based plan that addresses impaired waters (303d listed or TMDL waters) first be developed. This plan describes the watershed, water quality concerns and their sources, and a process for addressing those concerns through information outreach and implementation of BMPs over a specified time period.

The watershed based plan must be submitted to and accepted by the department and the U.S. Environmental Protection Agency. The accepted plan allows Section 319 grant funds to be used to support implementation of BMPs that, as described in the plan, reduce sediment, nutrients, bacteria and other pollutants from nonpoint sources in the watershed. When implementing Section 319 projects in MS4 areas, grant recipients are highly encouraged to work with their department project manager to ensure that proposed projects are consistent with Section 319 federal requirements and are considered ‘above and beyond’ MS4 permit requirements.

What is an MS4?

A municipal separate storm sewer system (MS4) is a conveyance or system of conveyances, including roads and highways with drainage systems, municipal streets, catch basins, curbs, gutters, ditches, paved or unpaved channels, or storm drains designated and utilized for routing of stormwater which:

  • Does not include any waters of the state as defined in section 644.016, RSMo.
  • Is owned and operated by the state, city, town, village, county, district, association or other public body created by or pursuant to the laws of Missouri having jurisdiction over disposal of sewage, industrial waste, stormwater or other liquid wastes.
  • Is not a part or portion of a combined sewer system.
  • Is not a part of a publicly owned treatment works.

Stormwater runoff often comes into contact with pollutants before being transported through MS4s and is often discharged untreated into local bodies of water. To prevent harmful pollutants from being washed or dumped into an MS4, some MS4 operators must obtain a permit with the department and develop a stormwater management program. Designation to obtain a permit and become a regulated MS4 is mostly determined by population and/or if the MS4 is in a U.S. Census-designated urbanized area. For a list of current regulated MS4s in Missouri, please review Missouri's Regulated Municipal Separate Storm Sewer Systems MS4s.  

How is the Section 319 grant program related to the MS4 permit program?

Both the Section 319 program and the MS4 program are aimed at reducing pollutant loading into surface waters. However, there are some important distinctions:

MS4 Program vs. 319 Program
  MS4 Program 319 Program
Purpose of Program Regulatory - Discharges from stormwater conveyance systems are "point sources" and are covered under a general or individual permit. Assistance - The 319 program support watershed planning and implementation of nonpoint source (NPS) BMPs through grants.
Scope of Program Effective in urban and suburban areas. Carried out in urban, suburban, rural and agricultural areas.

Section 319 Program Information and Requirements

Eligible applicants include cities, municipal and county governments, state agencies, nonprofit 501(c)(3) organizations, regional planning councils of government, higher education institutions and soil and water conservation districts. Other groups may also apply for grant funding by partnering with and through these organizations. Project proposals should include partners from other government agencies, nonprofit groups and other responsible entities, such as private for-profit subcontractors. Section 319 projects may have a maximum federal funding component of 60% of the total project cost; the remaining 40% of the total project cost must come from local matching funds in the form of cash donations or in-kind contributions from project partners.

Section 319 grant funds may be used to develop a department and EPA accepted watershed based plan that meets the requirements of the department’s nine-element watershed based plan checklist, or to implement an approved plan. BMPs should be selected as specified in the watershed based plan and must be implemented in the critical areas described in the plan. Section 319 grant-supported BMP projects usually either create cost-share programs or develop demonstration or implementation projects.

Cost-Share Programs

Section 319 grant funds may be used to develop and implement cost-share programs where the funds will provide a maximum reimbursement of 75% of the total BMP installation cost. At least 25% of the cost must be provided by the landowner/organization or other non-federal source as match. Design costs may be included in the cost-share project’s total cost and will be reimbursed after the department project manager has reviewed and approved the design. All cost-share work must be documented by bills or receipts outlining costs, which are reasonable and customary for work being done. Eligible costs include: cost of materials, labor charges (including landowner labor), contractor, consultant or third party charges, costs to modify existing equipment for a different use, fees for laboratory analyses and equipment rental fees.

Demonstration Projects

Demonstration projects showcase BMPs that introduce new nonpoint source reduction/removal techniques in the watershed and encourage buy-in from landowners and other local stakeholders for watershed planning and implementation. Depending on project specifics, and with department project manager approval, Section 319 may reimburse up to 100% of demonstration project costs with the following stipulations:

  • They must not have been implemented as part of a previous watershed Section 319 grant-funded demonstration or cost-share program.
  • They must be located in a critical area identified in the watershed-based plan.
  • They must be located on public land or any area where the public can access on a regular basis. Examples of locations suitable for demonstrations include parks, shopping plazas and common areas in subdivisions. Locations must be approved by the department project manager before submitting any invoices.
  • They must be used/showcased as part of an information outreach event.
  • They must be properly installed and maintained as discussed in this section.
  • Demonstration project implementation must be authorized in the grant recipient’s subaward agreement.

Implementation Projects

Implementation projects focus on implementing specific BMPs as prescribed in a department and EPA approved watershed-based plan to address specific water quality impairments. These projects must be located in a critical area identified in the watershed-based plan, must be properly installed and maintained and must be described in the subgrant agreement’s scope of work.

In situations where a BMP is installed to avoid maintenance or replacement costs of the existing infrastructure, the portion of the project that would be eligible under Section 319 is the difference between the cost for repair/replacement and the cost of totally retrofitting the infrastructure with the BMP.

For example:

  • If a building owner who needed to replace the roof was persuaded to install a green roof instead, the difference in cost between replacing the roof using materials comparable to the existing roof and installing a green roof would be eligible for Section 319 grant funds. However, if a roof that does not need to be repaired or replaced was converted to a green roof, then the project’s total cost would be eligible for Section 319 grant funds.
  • If a city that needed to replace a pipe holding a buried stream is instead interested in using Section 319 grant funds to daylight the stream, the difference in cost between replacing the pipe and daylighting the stream would be eligible for Section 319 grant funds. However, if the pipe was not in need of replacement but the city agreed to daylight the stream, the project’s total cost would be eligible for Section 319 grant funds.

In situations where serviceable infrastructure is demolished and/or removed, Section 319 will pay for those activities if they are needed to properly install a BMP. However, such demolition and/or removal can add a significant cost and must be justified by the positive impact the project will have on water quality. Before approving a project where serviceable infrastructure is demolished and/or removed, the department project manager may apply the criteria discussed below in Considerations When Choosing a BMP.

Examples of serviceable infrastructure being demolished and/or removed as part of a BMP’s installation include:

  • Removing concrete in an alley and installing a vegetative swale.
  • Removing concrete around parking lot storm drains and installing pervious pavement.
  • Removing parts of a roof and installing a green roof.
  • Removing a stormwater pond’s riser and installing a riser that releases less water.

Project Maintenance, Load Reductions and Invoicing

All BMPs installed with Section 319 grant or match funds must be checked and properly maintained during the remainder of the project period. The Section 319 program highly recommends that the grant recipient establish a maintenance program to cover the total service life of the installed BMPs. Examples of maintenance requirements include land management practices, vegetative practices and structural practices on residential land (five years) and structural practices on non-residential land (10 years).

When nonpoint source BMPs are implemented, the grant recipient must estimate pollutant load reductions using an approved method, such as the STEPL model, or other models or simple calculation methods. In some cases, calculating pollutant load reductions will not be possible; when these circumstances arise, they must be discussed with the department project manager.

To receive reimbursement for BMPs that have been implemented, an invoice for payment must be submitted to the department’s project and fiscal managers, along with the completed invoice form (financial assistance agreement Attachment A-2) and the following documents:

  • Financial Summary Sheet.
  • Copies of bills or receipts for each cost-share practice showing the total cost.
  • Copies of documentation and receipts for any other project costs requested for reimbursement
  • Pre- and post-work photos.
  • GPS coordinates or map showing the location of all practices in relation to adjacent roads.

Applicability with State and Federal Regulations

Section 319 grant funds may not be used to implement projects for the purpose of meeting any state regulations or National Pollutant Discharge Elimination System Storm Water Program requirements. Within an urban setting, these requirements most often apply to 10 CSR 20-6.200(1), 40 CFR 122.34, and 40 CFR 122.26, the regulation of Municipal Separate Storm Sewer Systems (MS4s). It is the grant applicant’s responsibility to know which regulations apply to a proposed project site.

The easiest way to ensure Section 319 grant funds are appropriately spent is to be cautious working on new construction or redevelopment sites, since those sites may fall under the MS4 regulations. Grant applicants  can work on such sites if the proposed project is classified as ‘above and beyond’ any permit requirements. The Section 319 program or MS4 program can help determine if a scenario meets the ‘above and beyond’ classification. For more specific information about the MS4 permit requirements and the types of projects that classify as ‘above and beyond’ contact MS4@dnr.mo.gov.

Urban Best Management Practice (BMP) Implementation

Considerations When Choosing A BMP

Grant recipients must get approval from the department project manager before committing funds to a specific BMP project or cost-share program. The following three conditions must be met for a BMP project or cost-share program to be eligible for Section 319 grant funds:

  • The project addresses a water quality problem outlined in the watershed-based plan.
  • The project is to be implemented in a critical area as defined by an approved watershed-based plan.
  • The project is described in the subaward agreement.
  • Other related criteria may need to be considered if aspects of these three conditions cannot clearly be decided.

Context of the BMP Site

Any urban implementation project should consult long-term planning documents, as well as the city, county or local planning and development authority before selecting site locations. This will help to guarantee specific BMP projects and cost-share programs align with the site’s long-term planning and zoning characteristics. For example, implementing filter strips across an area that is planned to be rezoned, or working on a street retrofit when local ordinances restrict such projects.

Whenever possible, the proposed project should have the support of local partners to make certain there is a commitment to maintenance and pursuing complementary projects. The department encourages grant recipients to take advantage of the many local stakeholders and encourage them to provide ideas to determine where local priorities overlap with the goals and opportunities identified in the watershed-based plan.

BMP Appropriateness

It is important to consider the type and placement of BMPs within a critical area to make sure they appropriately address the water quality pollutants of concern outlined in the watershed-based plan and do not function as spot fixes or temporary solutions for much larger issues. The department project manager must approve the BMPs to be implemented before Section 319 grant funds can be used.

For example, stabilizing streambanks without also implementing BMPs that slow, spread and infiltrate stormwater runoff would be ranked as a low priority for project value and funding.

Because stormwater runoff delivers additional pollutants to urban streams and contributes to streambank destabilization, stopping runoff from reaching streams is important in an urban setting. Section 319 grant funds cannot be used to solely address flooding concerns or remove flow from a stream channel. Rather, a project must implement BMPs to decrease polluted runoff before it reaches a Water of the State or an MS4 conveyance to be considered eligible – but reduced flooding may be a secondary benefit of that project. Examples include, but are not limited to:

  • Installing rain barrels or rain gardens in neighborhoods adjacent to streams.
  • Modifying a stormwater pond to allow more water to infiltrate into the ground.
  • Installing pervious pavement around parking lot storm drains and areas where snow is piled.
  • Installing a constructed wetland.
  • Installing a green roof.

Pollutant Load Reductions

The department expects projects to consider the ratio of BMP cost to pollutant load reduction and to make judicious use of limited grant funding. The department’s first priority is to improve water quality through the reduction of pollutant loads. The department will request that proposed projects provide the estimated pollutant load reductions based on the BMPs to be implemented. Projects that cannot demonstrate a load reduction will be ranked as low priority for project value and funding (exceptions will be made if a method for estimating a project’s reductions does not exist).

Load reductions can be estimated using EPA accepted tools such as STEPL or other models, or by using simple calculations based on credible values for a given BMP’s pollutant load reduction efficiency.

Section 319’s Preferred Urban BMP Projects

The department encourages grant recipients to work closely with the Nonpoint Source and Total Maximum Daily Load Sections to answer key questions about BMP selection (e.g., addressing a water quality problem, implementation in a critical area and description in the subaward agreement), before committing Section 319 grant funds. Because urban environments across Missouri have highly varied local MS4 requirements and watershed goals, a comprehensive list of pre-approved urban BMPs is not possible. If possible, consider using a system of BMPs to maximize pollutant load reductions. The department recommends that grant recipients in urban areas focus on two types of urban BMPs/cost-share projects: Low Impact Development and Retrofits.

Low Impact Development

Low Impact Development is an approach to land development (or re-development) that mimics nature to manage stormwater as close to its source as possible. Low Impact Development employs site design principles, such as preserving and recreating natural landscape features and minimizing imperviousness, to create functional and appealing site drainage that treats stormwater as a resource rather than a waste product. Because creating Low Impact Development site plans demands a background in project design, hydrology, soils and other disciplines, grant recipients interested in Section 319 funding must use a qualified professional engineer to develop these plans.

Low Impact Development designs will often recommend specific BMPs that complement the design by infiltrating runoff. Common examples of urban infiltration BMPs include green roofs, rain gardens and other bioretention features, rain barrels, porous pavement and bio-swales.


Retrofits provide an opportunity to add a water quality benefit to an existing site, structure or BMP, often by adding some of the BMPs discussed above. Within the urban environment, meeting water quality goals without retrofitting will be difficult. The use of Section 319 grant funds to assist local communities in retrofit strategy planning or implementation is appropriate.

The Center for Watershed Protection has published a manual titled “Urban Stormwater Retrofit Practices1,” which provides relevant details about a number of potentially eligible practices. The manual also provides input on finding water quality retrofits on the following landscapes:

  • Existing Ponds: Stormwater ponds can be retrofitted to include wetland features or have their riser modified to improve water quality.
  • Parking Lots: Both large and small parking lots can provide opportunities to add curb cuts, vegetated beds designed for stormwater infiltration, porous pavement and sand filters adjacent to the lot where runoff flows.
  • NPS Hotspots: Hotspots are areas with greater than normal concentrations of nonpoint source pollution. Hotspots are usually industrial and often make good sites for sand filters.
  • Transport Rights-of-Way: Large areas along highways and small areas like street medians may support infiltration practices or wetland features.
  • Individual Streets: Streets may be retrofitted to include porous pavement, infiltration practices and improvements to drainage swales.
  • Individual Roofs: Some existing roofs can be retrofitted to support a green roof.
  • Hardscape Landscapes: Tree boxes, tree lawns, porous pavement, and bioretention can provide infiltration opportunities in traditionally impervious areas.

Preferred Urban Outreach Activities

Outreach activities are required and are an important part of any urban Section 319 grant project. Considering the small pool of funds available for BMPs, outreach can be a means to extend a project’s reach to a larger segment of a watershed’s community and encourage people to take action or change their behavior. Outreach activity costs may not exceed 10% of a Section 319 federal grant award, must be project specific and must address a problem or goal outlined in the watershed-based plan. Outreach activities may include demonstration projects, informational events, training, and local environmental policy education. Outreach activities do not have to be held within a critical area, but they must focus on an issue that is pertinent to a critical area. Section 319 grant recipients are encouraged to review EPA’s “Getting in Step” manual2, which focuses on conducting watershed outreach campaigns.

Demonstration Projects

Demonstration projects showcase BMPs that introduce new nonpoint source management techniques in the watershed and encourage buy-in from local stakeholders for watershed planning and implementation. See requirements for demonstration projects in the Section 319 Program Information and Requirements section above. Costs for installation of pollutant load reduction BMPs are not impacted by the 10% outreach cap, but outreach efforts associated with the demonstration project are. Those outreach efforts must include on-site signage, and may also include informational field days, brochures, workdays, etc. 

Informational Events

Changing behavior can take a change in mindset, which is facilitated by informational outreach activities. Information outreach provides people the knowledge needed to make sound decisions that will ultimately benefit their community and the environment. Information outreach also helps identify the specific skills people need to implement or act on the subject, but does not require them to develop those skills. Examples of informational events are public meetings, displays at county fairs, field days and workshops on nonpoint source pollution and water quality. Informational events must meet all of the following conditions:

  • Convey general information about watersheds, improving water quality, nonpoint source pollution or BMPs. The intention is to change participants’ behaviors.
  • The behavioral change does not reflect or require the gaining of any particular skills on the part of the participants.

Examples of behavioral change include:

  • Ceasing to pour motor oil down storm drains.
  • Following the manufacturer’s directions when applying fertilizers or other chemicals at home.
  • Properly disposing of pet waste.
  • Switching to a more environmentally friendly product.
  • Properly using, operating and maintaining something such as a septic system or chemical applicator.
  • Learning about BMPs, excluding specific information about how to install them.

People who perform work that is required to conduct or support the informational event (e.g., laborers, classroom aides, presenters, etc.) are providing a service; therefore, their work and eligible expenses can be counted as match or reimbursed with Section 319 grant funds. However, event participants involved solely in a learning capacity are not providing a service; therefore, their time or expenses cannot be counted as match or reimbursed with Section 319 grant funds.


Training is an activity that imparts knowledge to participants and allows them to develop the skills necessary to complete or oversee work expected to be carried out during watershed planning or implementation (as documented in either the grant agreement or watershed based plan). Training includes activities where participants can earn Continuing Education Units or learn to install BMPs in the watershed. To be considered training, the event must meet the following criteria:

  • Allows the participant to meet continuing education/development credits from an approved certification program. EPA and the department encourage grant recipients who host training events/activities to work with as many certification programs as suitable for the subject matter.

Or, if the event does not qualify for continuing education/development credits, it must meet all of the following conditions:

  • Be led by professionals discussing their field of expertise.
  • Be structured such that participants receive needed skills and knowledge that are detailed and specific enough to work on an objective required of the watershed planning process or from the draft or approved watershed based plan. Examples include:
    • A rain garden training course where participants learn how to build a rain garden by actually constructing one.
    • A water quality sampling training course during which participants learn how to sample by physically taking and reading or analyzing samples.
    • A training course on low-impact land-use planning during which participants learn how to incorporate new planning tools that promote sustainability and other low-impact concepts.
    • A training course on hydromodification during which participants learn the consequences of channelization, drainage or impervious surface and how to incorporate new techniques that decrease long-term maintenance costs and benefit water quality and stream health.

Participants must be in a position to use the received skills and knowledge in the project area. Examples include:

  • Homeowners learning how to install a specific BMP on their property.
  • Land-use planners and other relevant officials learning how to incorporate LID within their jurisdiction.

Project trainings must be pre-approved by the department project manager to qualify and be documented as training. If approved, expenses related to organizing the training may be reimbursed with grant funds or counted as nonfederal match with the required documentation. Expenses related to training activity presenters may be reimbursed with grant funds or counted as nonfederal match, but the presenter cannot be a federal employee or paid through federal funds.

Local Environmental Policy Education

Grant recipients are encouraged to create working relationships with local officials and to inform them about new ideas and concepts that reduce nonpoint source pollution, but those actions must help achieve a goal in the watershed-based plan. Examples of this strategy include:

  • Informing local officials and planning departments on incentives they can give to developers to promote green development. A good example is a city expediting a permitting process for green development.
  • Informing landowners and drainage board members about the consequences of hydromodification and the benefits of two-stage ditches and other alternative maintenance techniques for legal drains.

In addition, watershed groups can work with local officials on ordinances; however, Section 319 grant funds cannot be spent on ordinance development or revision. Ordinances are especially important tools in urban watersheds, because each year new development often exceeds conservation efforts. Section 319 grant funds can be spent on:

  • Informational events and training courses that inform local officials about needed ordinances or ordinance changes.
  • Researching ordinance topics and creating ordinance recommendations; however, the watershed group’s delivered work product must not be ordinance language.
  • Informational events and training courses to inform the public and local officials on research and recommendations conducted on behalf of a local entity.

BMP Design Standards and Specifications

BMPs funded with Section 319 grant funds must be constructed in accordance with standards and specifications. The source of those standards and specifications must be provided to the department project manager for review.
There currently is no widespread acceptance of urban BMP standards and specifications. The department will consider standards and specifications from non-traditional sources, such as non-governmental websites, other state government websites and BMP contractors or manufacturers, if the source of the standards and specifications is properly documented. The department reserves the right to reject proposed standards and specifications. This would most likely occur if the department believes that a proposed BMP’s standard and specification is inconsistent with other standards and specifications for the identical BMP or if the standard and specification are applied in a manner inconsistent with Section 319 policy and federal requirements. If you have any questions about the appropriateness of standards or specifications, please contact the department project manager.

Nothing in this document may be used to implement any enforcement action or levy any penalty unless promulgated by rule under chapter 536 or authorized by statute.

For more information