National Pollutant Discharge Elimination System Permit Program (NPDES)


In 1990, the U.S. Environmental Protection Agency (EPA) published regulations requiring large and medium-sized municipalities to obtain National Pollutant Discharge Elimination System (NPDES) Permit Program operating permits for their Municipal Separate Storm Sewer Systems (MS4). These “Phase One” rules also required stormwater permits for a specified list of industries, and for construction sites five acres or larger in size. Prior to 1990, EPA regulations only required permits for traditional point sources of pollutant discharge, such as wastewater treatment plants and industrial process wastes.

In 1999, EPA extended the permit requirements to smaller municipalities (including St. Johns County). The “Phase Two” requirements are considerably less cumbersome than those for the Phase I counties and cities. The Phase Two rules also lowered the threshold for construction sites from five acres to one acre or larger. In October 2000, EPA delegated the NPDES program to the Florida Department of Environmental Protection (FDEP).

Phase Two Permits

The NPDES Phase Two permit is unlike typical EPA permits in that, rather than dictating to counties and cities their permit requirements, the local governments were presented with six Minimum Control Measures and allowed to select their own Best Management Practices (BMPs) and Measurable Goals for attaining those minimum measures that constitute our Stormwater Management Program.

Many of the permit program measures involve education – educating residents about how they can help prevent stormwater pollution, educating builders and businesses about ways they can prevent pollution, and educating county staff on pollution prevention. Other measures involve specific actions on the part of the County, such as storm sewer system operation and maintenance, recycling, construction and illicit discharge inspections, storm drain marking program, mapping the County’s stormwater outfalls, and application of BMPs at County facilities.

Control Measures

Six Minimum Control Measures

  1. Public Education and Outreach – Perform educational outreach regarding the harmful impacts of polluted stormwater runoff.
  2. Public Participation/Involvement Comply with State and local public notice requirements and encourage other avenues for citizen involvement.
  3. Illicit Discharge Detection and Elimination – Implement a plan to detect and eliminate any non-stormwater discharges to the Municipal Separate Storm Sewer System (MS4) and create a system map showing outfall locations. See the Glossary for more information.
  4. Construction Site Runoff Control – Implement and enforce an erosion and sediment control program for construction activities.
  5. Post-Construction Runoff Control – Implement and enforce a program to address discharges of post-construction stormwater runoff from new development and redevelopment areas. (NOTE: This minimum control measure is met by the State’s stormwater permitting program under the Water Management Districts, as a “qualifying alternative program,” thus there is no additional requirement for St. Johns County for this measure.)
  6. Pollution Prevention / Good Housekeeping – Implement a program to reduce pollutant runoff from municipal operations and property and perform staff pollution prevention training.

Other Measures Involve Specific Actions on the Part of the County

  1. Storm sewer system operation and maintenance
  2. Recycling, construction and illicit discharge inspections
  3. Storm drain inlet marking program
  4. Mapping the County’s Stormwater outfalls
  5. Application of Best Practice Measures at County facilities

St. Johns County’s Permit Status

The counties and cities identified as “Phase II MS4 operators” are required to obtain coverage under an NPDES general permit (known in Florida as a “generic” permit). The County was required by the Phase II rules to submit to FDEP a Notice of Intent (NOI) to utilize the Generic Permit for Stormwater Discharge from Phase II Municipal Separate Storm Sewer Systems. In their NOI’s, the applicants were required to describe the BMPs they had selected to achieve the six Minimum Control Measures. On June 23, 2003, the FDEP approved the St. Johns County NOI, and our permit became effective. A new permit was approved by the FDEP and came into effect on January 16, 2008.

Ongoing Requirements

The rules do not require all permitted BMPs to be fully effective upon permit issuance. Each permittee will spend the first five-year permit term developing and implementing the various BMPs for their Stormwater Management Programs. We are required to submit to FDEP an annual report for each of the first five years, describing our progress in implementing our BMPs, FDEP in turn conducts reviews of the submitted annual reports, MS4 audits and site inspections. During the subsequent permit cycles, the permittee spends the majority of the time continuing, evaluating, and expanding upon programs that were created during the previous permit term. Many of the permit requirements that were fully implemented during the first five years become projects that are reported on and kept track of on an annual basis. Those projects may only have had reporting requirements during the last few years of the original permit, but need to be monitored yearly for remaining permits to ensure that the programs remain in effect.

Glossary of Terms

Best Management Practices (BMP)

Any activities, structural solutions, maintenance procedures, prohibition against certain activities, and other management practices intended to prevent or reduce the pollution of surface waters or the County’s MS4. BMPs include but are not limited to: treatment facilities to remove pollutants from stormwater; operating and maintenance procedures; facility management practices to control runoff, spills or leaks of non-stormwater, waste disposal, and drainage from raw materials storage; erosion and sediment control practices; the prohibition of specific activities, practices, and procedures; and other such actions as the County or City determines appropriate and necessary for the control of pollutants.

Illicit Discharge

Any direct or indirect discharge to the County’s MS4, Waters of the U.S., or Waters of the State that is not composed entirely of stormwater, unless exempt pursuant to City or County Ordinance (some discharges, such as firefighting activities, are unavoidable, and are not prohibited.) Any discharge in violation of a NPDES permit also constitutes an illicit discharge. Illicit Discharge

Nonpoint Source Pollution

Nonpoint source (NPS) pollution, unlike pollution from industrial and sewage treatment plants, comes from many diffuse sources. NPS pollution occurs when rainfall, snowmelt, or irrigation runs over land or through the ground, picks up pollutants throughout the watershed, and deposits them into rivers, lakes, and coastal waters or introduces them into ground water. Imagine the path taken by a drop of rain from the time it hits the ground to when it reaches a river, ground water, or the ocean. Any pollutant it picks up on its journey can become part of the NPS problem. Essentially, anything we put on the ground will eventually find its way into our surface waters.

NPS pollution is widespread because it can occur any time activities disturb the land or water. Septic systems, urban runoff from streets and yards, construction, recreational boating, agriculture, forestry, grazing by livestock, physical changes to stream channels, and habitat degradation are all potential sources of NPS pollution. Careless or uninformed household waste management also contributes to NPS pollution problems.

Municipal Separate Storm Sewer System (MS4)

A conveyance or system of conveyances designed for conveying stormwater:

  • including, but not limited to, roads with drainage systems, streets, catch basins, curbs, gutters, ditches, manmade channels, or storm drains,
  • owned or operated by a local government,
  • that discharges to Waters of the United States, Waters of the State, or connects to other MS4s (of other cities or counties).

The word “separate” distinguishes most local government storm sewer systems from some of the older systems that were combined with “sanitary” sewers. These systems (called “combined sewers”) often experienced overflows of untreated sewage during storms, and are no longer built or permitted.

The legal definition of MS4 also includes any detention ponds, inlets, and other structures that are part of the stormwater conveyance system.