Coast of North Carolina: The frequency and intensity of coastal storms can influence coastal wetland types and distribution through erosion, deposition of sediments and salinity. (U.S. Fish and Wildlife Service)

The Environmental Protection Agency proposed a rule Tuesday that would give the federal government regulatory authority over millions of acres of wetlands and about 2 million miles of streams.

The proposal, which is subject to a 90-day comment period slated to begin in a few weeks, would lead to stricter pollution controls on some of these areas and aims to resolve a long-running legal battle over how to apply the Clean Water Act to the nation’s intermittent and ephemeral streams and wetlands.

“These places are where we get our drinking water, and where we hunt, fish, swim and play,” EPA Administrator Gina McCarthy said as she announced the proposed rule.

Environmentalists argue that these waters are critical to both fish and waterfowl, even if they are dry for parts of the year. Land developers and some farmers, by contrast, say the process of obtaining a federal permit to conduct their activities imposes an unnecessary burden on their operations.

The question of which isolated streams and wetlands qualify for protection under the Clean Water Act has been in dispute for a decade. The Supreme Court has issued two decisions, and the George W. Bush administration issued guidance in 2003 and 2008 limiting the scope of the act. The Obama administration delayed issuing a rule on the matter during its first term in part because of fierce objections from business interests.

All ephemeral and intermittent streams, and the wetlands that are connected or next to them, will be subject to federal oversight under the proposed rule. The agency is asking for public input on whether to require federal permits for a group of “other waters,” mainly wetlands such as those in the prairie pothole region.

In a telephone interview with reporters, McCarthy sought to address concerns from farmers and developers that the proposed rule is an overreach, expanding the jurisdiction of the Clean Water Act.

“They were concerned about an expansion of the Clean Water Act — there has not been,” she said. The farm and developing lobbies were also concerned that current exemptions they enjoy under the act would be eliminated, and under the rule they would not.

Jo-Ellen Darcy, the assistant secretary of the Army civil works, which worked with the EPA in writing the proposal, also sought to reassure opponents, asserting that they worked with the Agriculture Department in its development.

“In the last three years, this has been an unprecedented undertaking for the two agencies,” Darcy said. She said some farming practices over that time actually helped improve water quality, and those were taken into consideration.

About 60 percent of the miles making up U.S. streams only flow seasonally, or after rain.

“Today’s proposal speaks to the heart of the Clean Water Act — making rivers more fishable and swimmable,” said Trout Unlimited President Chris Wood in a statement. “The waters affected by today’s proposal provide vital spawning and rearing habitat for trout and salmon. Simply stated, the proposal will make fishing better, and anglers should support it.”

Intermittent and ephemeral streams provide critical fish habitat out West. They account for 94 percent of Arizona’s streams, according to the EPA, and 88 percent of those in New Mexico. These streams provide the flow for larger rivers and spawning and rearing habitat for young fish and insects; they also help to determine the quality of downstream habitat for fish.

Under the rule, the EPA and U.S. Army Corps of Engineers will have to evaluate the environmental impact of an activity that could impair one of these waterways, though the Clean Water Act exempts farming activity that does not involve discharging a pollutant. In addition, the new proposal exempts farmers who are undertaking one of 53 approved conservation measures from having to seek a federal discharge or fill permit.

Kevin Kelly, president of the National Association of Home Builders, criticized the rule as federal overreach.

“EPA was told to make changes to the rule so that everyone understands exactly when a builder needs a federal wetlands permit before turning the first shovel of dirt,” said Kelly, a home builder and developer from Wilmington, Del. “Instead, EPA has added just about everything into its jurisdiction by expanding the definition of a ‘tributary’ — even ditches and man-made canals, or any other feature that a regulator determines to have a bed, bank and high-water mark. It’s a waste of taxpayer resources to treat a rainwater ditch with the same scrutiny as we would the Delaware Bay.”

Whit Fosburgh, president and chief executive of the nonprofit Theodore Roosevelt Conservation Partnership of hunting and fishing organizations, extolled the virtue of clean water.

“Headwater streams . . . that is where all the fish come from,” he said. “All of them spawn in headwater streams triggered by snow melt and other runoff. We’ll hear a lot of talk about the economic impact of the rule.” Hunting and fishing is a $2-billion-a-year enterprise, generating more than $125 billion in state and federal taxes.

Fosburgh applauded the EPA and Army Corps of Engineers for the proposed rule. “We actually wanted to make it even stronger,” he said.