WASHINGTON — The Environmental Protection Agency proposed a rule Tuesday that would give the federal government regulatory authority over millions of acres of wetlands and roughly 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. 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.

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.

McCarthy, addressing concerns by developers and some farmers, said “there has not been an expansion of the Clean Water Act,” nor would current exemptions would be eliminated.