A federal judge here yesterday approved an agreement between three environmental groups and the Environmental Protection Agency that gives EPA more time to devise toxic pollutant discharge regulations, and also strengthens the agency's hand in setting the standards.

In putting the court's imprimatur on the December agreement between EPA and the Natural Resources Defense Council, the Environmental Defense Fund and the Citizens for a Better Environment, U.S. District Court Judge Thomas A. Flannery rejected the opposition of some of the nation's largest industries.

The pact sets a variety of dates later this year and next year, by which time EPA is required to have set standards for 34 industries on the quantities of 65 toxic chemicals they can discharge into the nation's waterways. The new deadlines are generally six months to a year later than those previously set by EPA.

At the same time, the new agreement gives EPA the right to try to identify toxic pollutants other than the 65 previously named in 1977 amendments to the 1972 Federal Water Pollution Control Act. In addition, EPA now has the right to set antipollution standards to protect specific bodies of water, not just to set rgeulations for the quantities of the discharges.

James T. Banks, a lawyer for the Natural Resources Defense Council, said the agreement represents some trade-offs for environmentalists. The environmental groups agreed to the later dates for setting the discharge regulations in the hope that the standards devised "will be done better" than if they had to be completed by unrealistically early deadlines, he said.

The original deadlines were set three years ago. But Banks said that those dates proved unworkable because of the "very expensive and complex procedures" that have to be used to set guidelines for the discharge. The regulations affect the coal mining, iron and steel, petroleum, pesticide and rubber industries, among others.

Richard Schwartz, a lawyer who represented the American Iron and Steel Institute and other industries in the case, said an appeal of the Flannery ruling would be "seriously considered."

He had argued, among other things, that Congress, in passing the 1977 water quality amendments, intended to supersede the 1976 deadlines and provisions under which EPA should set the discharge standards and that a court should not now intervene.

He predicted that EPA will not be able to meet the new deadlines, or, if it does, would use the deadlines to "short-circuit the administrative rulemaking process" under which the public and industries can voice their opinions about the EPA proposals.