Communities within the Delta region use the estuary to dispose of sewage and stormwater. While these discharges are subject to state and federal regulation, many local entities are frequently in violation of their permit requirements.

Toxicity in urban stormwater runoff includes harmful substances from streets, lawns and gardens, such as automotive oil, zinc from brake residue, and pesticides. In fact, urban areas contribute more pesticide runoff than agriculture in many parts of the state, including the Delta. According to the California Department of Pesticide Regulation, in the Sacramento Valley between 1995 and 2006, urban application of pesticides was 21 percent greater than for agriculture.

To get a picture of how urban water discharges can affect Delta wildlife, UC Berkeley Professor Donald Weston studied the effects of pyrethroids, a common household pesticide contained in urban stormwater and wastewater discharges and known to harm aquatic species, and a native crustacean to the Delta, Hyalella azteca. In his sampling, Weston found that virtually all urban stormwater runoff contained pyrethroids, typically at about 4 times the concentration that would paralyze Hyalella. Meanwhile, the study found that typical wastewater treatment plant effluent in the Delta contains pyrethroids at about 0.5-1.5 times the concentrations that cause Hyalella paralysis.

Although it is impossible to keep all pollutants out of the Delta waters, local water dischargers often fail their legal responsibility to meet permit requirements and stop preventable pollution. According to Central Valley Regional Water Quality Control Board records, municipalities across the Delta have continuously violated stormwater and wastewater discharge permit requirements. Keeping in mind that those records do not necessarily reflect all violations, even those limited records show repeated violations across the board. For example, from 2007 to 2012, records show that at least eleven municipalities have over 100 violations, among them the City of Stockton (196 violations), San Joaquin County (175 violations) and even the tiny Town of Discovery Bay (140 violations). While violations range in magnitude from exceeding maximum allowable effluent discharges for harmful nitrates or bacteria, to smaller reporting and monitoring violations, all show a callous disregard by local municipalities for the Delta ecosystem and the species it supports.

The Sacramento region was historically a large polluter and each day discharged millions of gallons of partially treated sewage into the Delta. Sacramento is now in the final stages of upgrading its sewage treatment facilities to reduce ammonia and other discharges, in large part due to pressure from the Coalition for a Sustainable Delta, environmental interests and other downstream water users.

Delta municipalities are often also in violation of their separate municipal stormwater sewage system (MS4) permits. Pollutants from MS4s in the Delta in excess of allowable levels include aluminum, copper, iron, zinc, E. coli, fecal coliform, and dissolved oxygen, all of which can have severe detrimental effects on the Delta ecosystem.