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.

Every day, up to one billion gallons of partially treated sewage is flushed into the Sacramento San Joaquin Delta. Municipal wastewater is directly discharged to Delta waterways from over 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.

As Northern California’s population continues to expand, these discharges and their impact on the Delta’s ecosystem and fisheries continues to grow. Wastewater discharges affect the quantity, quality, and temperature of water flows. As well as increased pollution such as ammonia, heavy metals and pharmaceuticals being discharged in the estuary where they harm fish and wildlife.

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 sites are also a major source of storm-water runoff. 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.

Visit our Violating the Delta page for more detailed information on major pollution in the Delta.