The effects of human development on the Delta ecosystem are numerous. Local stakeholders in the Delta never fail to highlight the impacts of water pumping operations, but their narrow focus on water exports ignores the pollution they are putting into the estuary and its effects on water quality and wildlife.

Municipal wastewater is directly discharged to Delta waterways from more than 300 municipal sources. Many of these municipal discharges are located in the heart of the Delta, where they release directly into the critical habitat of endangered fish species. These discharges lead to increased pollution, including toxic contaminants such as ammonia, heavy metals, and even pharmaceuticals. As population continues to increase in the region, so will wastewater discharges and their impacts on the estuary.

Consider the following:

  • Every day, up to one billion gallons of partially treated sewage is flushed into the Sacramento San Joaquin Delta.
  • There are at least 52 wastewater discharge sites in the Delta and an additional 25 stormwater discharge sites, each contributing to the pollution of the estuary.
  • A 2008 investigation by the Associated Press revealed the presence of pharmaceuticals in the drinking water of major metropolitan areas. Scientific evidence suggests even small amounts of such substances – including estrogen, antibiotics and heart medications – may adversely affect habitat and fish species. A 2014 study detected concentrations of pharmaceuticals, including carbamazepine, fluoxetine, and trimethoprim, near main Delta wastewater facilities in concentrations that could be chronic to aquatic organisms within the Delta.
  • As a result of Coalition efforts, Sacramento Regional Sanitation District is in the process of updating their wastewater treatment facilities.

In addition, more than 150 commercial operations, such as mining and other industrial facilities are currently permitted to discharge processed wastewater in and upstream of the Delta. These facilities release as much as 5 million gallons of wastewater each day and have a significant impact on delta water quality, the ecosystem and its fisheries. Industrial materials such as fuel, oil and debris are carried by storm runoff from these facilities into the Delta water ways.

Thousands of abandoned mines also litter the California landscape. Many of these mines are in the Sierra foothills and discharge harmful chemicals such as mercury, chromium, cyanide and asbestos that can pollute drinking water and harm fish and habitat. Runoff from these mines continues to contaminate Delta watersheds and downstream environments contributing to unsafe mercury levels in fish.

“It is clear these abandoned mines pose a threat to public health and safety – and they must be cleaned up.”

– U.S. Senator Dianne Feinstein 

But little progress has been made in doing so.

The U.S. Department of Transportation Maritime Administration (MARAD) was found by a federal judge to be illegally polluting and storing hazardous waste in the San Francisco Bay. MARAD is in charge of decaying naval vessels stored in Suisun Bay, which are discharging toxic heavy metals into the waters.


An estimated 20 tons of heavy metals including lead, zinc, copper and cadmium have fallen, blown or washed off the obsolete ships, according to the Federal government’s own analysis. If not cleaned up, they would have shed an additional 50 tons into Suisun Bay.

Under the court settlement  MARAD must clean and remove all of the obsolete ships from the Suisun Bay by September 2017. MARAD’s September 30, 2015 update states that MARAD has currently removed 60 non-retention vessels from the bay.

Sources: Sacramento Bee, Associated Press

*Information related to the Major NPDES dischargers in the Sacramento/San Joaquin Delta Watershed was retrieved from the California Integrated Water Quality System Project (CIWQS) Regulated Facilities Report available on the website of the State Water Resources Control Board as well as the respective NPDES permits issued to each facility.