"The agency is aware of the growing homelessness crisis developing in major California cities, including Los Angeles and San Francisco, and the impact of this crisis on the environment."

"Based upon data and reports, the agency is concerned that California’s implementation of federal environmental laws is failing to meet its obligations required under delegated federal programs."

Wrote EPA Administrator Andrew Wheeler to California Governor Gavin Newsome, quoted in "EPA tells California it is ‘failing to meet its obligations’ to protect the environment" (WaPo).
San Francisco officials reject the idea that they have failed to capture objects such as needles because they send sewage and street runoff to the same pipes. This combined discharge is treated at one of the city’s sewage treatment plants, where pollutants are captured or treated before being released to the San Francisco Bay or the Pacific Ocean.

“We have our challenges in San Francisco around homelessness,” San Francisco Mayor London Breed’s communications director, Jeff Cretan, said in response to Trump’s comments aboard Air Force One. “But in terms of needles flowing into the bay, it’s absolutely ridiculous.”
In terms of excrement flowing into the bay, it’s not absolutely ridiculous.
San Francisco is one of the few major cities with sewers that combine stormwater and sewage flows that is not operating under a federal consent decree.

Drawing on public databases and press reports — including a NPR report in August that “piles of human feces” are now visible on sidewalks and streets in San Francisco — Wheeler noted that even California’s own government has posted studies noting that human waste can increase bacteria levels in water off its beaches.

He detailed a litany of federal water quality violations across the state, saying California “has not acted with a sense of urgency to abate this public health and environmental problems.”

The examples include a “years-long practice” of San Francisco routinely discharging more than a billion gallons of combined sewage and stormwater annually into San Francisco Bay and the Pacific Ocean without treating it for biological contaminants....

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