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"Piles of human feces on sidewalks and streets" pose a threat to water quality, Wheeler said in a letter to California Gov. Gavin Newsom that criticizes San Francisco, where Newsom was once mayor, for routinely discharging inadequately treated sewage into the Pacific Ocean.
The Trump administration official insisted on a detailed plan to address the matter within 30 days.
The agency will have to take action otherwise, Wheeler said.
Newsom asked President Trump earlier in September to approve more housing vouchers to combat homelessness. "Shelter solves sleep, but only housing solves homelessness," the governor wrote in a letter.
The missive requested that Trump not only provide 50,000 more housing vouchers through two existing programs but also asked him to increase the value of the vouchers to coincide with rising rent costs.
FOX Business' Blair Shiff and the Associated Press contributed to this report.