The rule allowed fertilizers, pesticides and industrial chemicals to flow into small streams, marshes and wetlands. The judge warned of environmental harm.

A federal judge on Monday struck down a Trump-era environmental rulethat drastically limited federal restrictions against pollution of millions of streams, wetlands and marshes across the country.

The Biden administration had already begun the lengthy process of undoing the policy, which President Donald J. Trump established in 2020 after farmers, real estate developers and fossil fuel producers complained that Obama-era rules had saddled them with onerous regulatory burdens. Mr. Trump’s policy allowed the discharge of pollutants such as fertilizers, pesticides and industrial chemicals into smaller streams and wetlands.

But on Monday, Judge Rosemary Márquez of the United States District Court for the District of Arizona found “fundamental, substantive flaws” with the Trump administration’s policy and said that it was in conflict with the 1972 Clean Water Act. She warned of the “possibility of serious environmental harm” if the Trump rule remained in place.