MS4 means Municipal Separated Storm sewer system. For a municipality running separate storm and sewer systems, there are required activities to protect and conserve natural resources and the environment in general. The system includes ditches, curbs, gutters, storm sewers, and similar means of collecting or conveying runoff that is completely separate from a wastewater collection system and treatment plant. In other word, the water from precipitation (rain) is not treated. It falls on streets and other surfaces, goes into storm drains and directly to waterways and Galveston Bay.
This water is where recreational fishing and swimming occur; since it is not treated, we should protect and care for the storm system. More information on this permit, activities and public outreach efforts supported by this permitting process is available in this guide (PDF).