Harris County, Harris County Flood Control District, and the City of Houston form the Stormwater Management Joint Task Force (JTF). In February 2009, Texas Commission on Environmental Quality (TCEQ) issued the JTF a joint Municipal Separate Storm Sewer System (MS4) permit that authorizes the JTF to discharge stormwater from its MS4. The permit requires the JTF to develop and implement programs to reduce pollutants from its stormwater to the maximum extent practicable. These programs include household hazardous waste collection, public education, illicit discharge detection, and elimination, monitoring and sampling, and areas of new development and significant redevelopment.

Industrial facilities with stormwater discharges associated with industrial activity, as defined by TCEQ, must obtain coverage with either an individual permit or with the Texas Pollutant Discharge Elimination System Multi.-Sector General Permit (MSGP). Under these permits, industrial facilities have certain requirements designed to reduce pollutants in stormwater run-off.

The construction general permit is TXR 150000. This permit requires construction site operators to implement best management practices (BMPs) that will reduce pollutants in stormwater run-off. Operators of construction sites that will disturb five or more acres or that are part of a common plan of development or sale that will disturb five or more acres (large construction sites) must submit a TCEQ NOI form to TCEQ. Operators of construction sites that will disturb one or more acres but less than five acres or that are part of a common plan of development or sale that will disturb one or more acres but less than five acres (small construction sites) must post a Construction Site Notice.