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Lee County


Municipal Separate Storm Sewer System (MS4) Permit

The following is a brief discussion of the MS4 Permit (FLS000035) as it pertains to Lee County. 


In 1995 Lee County and 13 co-permittees applied for a municipal separate storm sewer (MS4) permit from the USEPA.  The permit (FLS000035) became effective in 1998 and was renewed by DEP in 2003, note the FDEP assumed control of the state-wide NPDES program in 2000.  As part of the regular permit renewal and Year 4 Annual Reporting process Lee County submitted a second renewal application to FDEP in 2008.  The 3rd cycle Permit FLS000035-03 was issued in 2011 and modified in 2013 to include Lee County and 21 co-permittees.


In October 2000, EPA authorized the Florida Department of Environmental Protection (FDEP) to implement the NPDES stormwater permitting program.  Under the authority  set forth in Section 403.0885, Florida Statutes (F.S.), FDEP issues permits to municipalities with populations over 100,000 to regulate waste water and stormwater (also referred to as a municipal separate storm sewer system or MS4) treatment facilities.  The NPDES stormwater program regulates point source discharges of stormwater into surface waters of the State of Florida from certain municipal, industrial and construction activities.  As the NPDES stormwater permitting authority, FDEP is responsible for promulgating rules and issuing permits, managing and reviewing permit applications, auditing annual reports submitted by permittees and performing compliance and enforcement activities.


DEP requires Lee County and co-permittees to develop and report on elements of the permit including:

·         Stormwater system inspection of the MS4 as well as compliance inspection of any new development or industrial site that discharges into the permitted MS4.

·         Stormwater system maintenance records,

·         Water quality and stormwater system compliance monitoring,

·         Enforcement of stormwater BMP application on development and industrial sites.

·         Public education for the purpose of keeping citizens aware of stormwater pollution impacts as well as educating the industry on the proper application of stormwater pollution controls. 

·         Discover and manage (prohibit) Illicit Discharges to the stormwater system.  This is accomplished through monitoring, proactive inspections and enforcement activities against those who discharge illicitly.  This is to control non stormwater discharges to the MS4.

·         Inspection and Investigation of Illicit Discharges and Improper disposal.  This is to target older infrastructure, Industrial and Mixed Use areas, Areas with on-site Sewage disposal systems and areas upstream of sensitive or impaired water bodies.

·         Verify Multi-Sector permits at industrial facilities and report those failing to obtain coverage to FDEP.

·         Illicit Discharges or Oils, Toxics and Hazardous Waste are to be controlled via a plan with quantities reported in the annual reports.

·         Illicit Discharges of Sanitary Wastes are to be reduced and eliminated in conjunction with the efforts of the local utilities with quantities and events reported in Annual Reports.

·         Industrial and High Risk Facility inventory and inspections to include the outfalls with reports annually.  Enforcement action to be taken against facilities violating the appropriate protocols.  This may include the monitoring or to require results of monitoring of regulated industrial facilities.

·         Perform inspections and recordkeeping related to construction site activities.

·         Develop and Maintain procedures to assure develop and permit applicants for re-development acquire proper stormwater permits, including ERP and GP for Large and Small construction sites.

·         Provide Construction Site Operator training such as the Florida Stormwater Erosion and Sediment Control Inspector’s Certification classes.  Provide training to municipal employees in the recognition and reporting of Illicit Discharges.

·         In addition to providing the Seasonal Loadings and Event Mean Concentration Estimates as required by the permit, Lee County Monitors the ambient quality of its surface waters.  This may be seen on the Lee County Web site on the Lee County Environmental Laboratory, Lab Data page.

Permit Renewal:

The Permit is renewable as part of the fourth annual report by requesting renewal.  Any requirements to be added to the permit are spelled out during the Draft permit by the permitting agency (FDEP).  This is one of several points in the process where the public may make commentary on the draft permit.

Annual Reports:

The permit requires Annual Reports to be submitted detailing quantities of activities which have taken place during the reporting period.  In the Annual Report the monitoring results are summarized as well as any problems found with the Storm Water Management Plan in the reporting period.


The majority of materials related to the permit are posted on the Lee County Web site:  The information found there includes the permits, including drafts, minutes from monthly co-permittee meetings and Annual Reports.

New In This Cycle:

There are existing and upcoming regulatory changes to the permit concerning Total Maximum Daily Loads (TMDLs) and Basin Management Action Plans (BMAPs).  TMDLs relate to state defined impaired waters and the quantity of impairment required to be removed for the water body to achieve compliance.  The BMAP is the descriptive plan outlining the specific implementation tasks and the responsible parties how they will be implemented.  Both the TMDL and BMAP will be tied directly to permit responsibilities for each co-permittee.