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The Environmental Protection Agency and the Army Corps of Engineers, which worked together to write the original Obama water rule, are expected to issue a new, looser replacement regulation by the end of this year. It is expected that the new measure, still being developed, will retain federal protections for larger bodies of water, the rivers that drain into them and wetlands that are directly adjacent to those bodies of water.

But it will quite likely strip away protections for streams that run only during or after rainfalls, and for wetlands that are not adjacent to major bodies of water or connected to them by a surface channel. Those changes would represent a victory for farmers and rural landowners who aggressively lobbied the Trump administration.

Lawyers said the interim period between the repeal of the Obama rule and the implementation of the new Trump rule this year could lead to regulatory confusion for farmers and landowners.

“The Obama clean water rule had very clear lines defining which waters are protected by the Clean Water Act, versus which waters are not, while repealing the rule means replacing those lines with case-by-case calls,” said Blan Holman, an expert on water regulations with the Southern Environmental Law Center.

Mr. Holman said the administration was replacing “clear, bright-line rules” with a case-by-case system. “This will be very unpredictable,” he said.

Legal experts also predicted a barrage of lawsuits across the country.

Under the provisions of the Clean Water Act, legal challenges must be heard in Federal District Court, which is based at the state level, rather than federal appeals court. Richard J. Lazarus, a professor of environmental law at Harvard Law School, said that meant that opponents of the Trump administration would focus their challenges in states they perceived as friendly.

“It’s going to be chaos,” Mr. Lazarus said. “We’re going to see suits brought all over the country.”

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