In an emotional farewell speech, William D. Ruckelshaus yesterday told Environmental Protection Agency employes that the administration will not propose deep cuts in the agency's budget in the coming fiscal year, but neither will there be additional money to help the EPA meet new responsibilities.

"EPA is going to be frozen, like all domestic agencies," he told more than 1,000 agency employes gathered in a downtown auditorium for an annual awards ceremony. The word came from President Reagan at a meeting Wednesday, Ruckelshaus said, and there is little room for appeal.

But the news came as a relief to many EPA employes, who had widely expected that Reagan's second term would signal a return to the budget-slashing practices of the administration's first two years.

In the wake of Ruckelshaus' resignation last week, congressional sources said that cuts of up to 30 percent had been proposed for the EPA.

A cut of that size "isn't going to happen," said Ruckelshaus, who strongly denied yesterday that budgetary constraints had anything to do with his decision to leave.

It was the second time Ruckelshaus has said goodbye to the EPA, which he also headed from 1970 to 1973. He returned last year to rescue the agency from a fiery controversy over management policies that had led to the resignations of then-administrator Anne M. Burford and more than a dozen other political appointees.

EPA employes gave Ruckelshaus a tumultuous welcome then, and hundreds turned out yesterday to say farewell to the man who is widely credited with restoring the agency's morale and policy footing.

Standing on a stage decorated with a huge banner bearing the words "Thanks, Bill!," Ruckelshaus said he believes that "the agency is in good shape."

"Resources are up and I couldn't feel better about the EPA," he said.

But his 18-month tenure has been a disappointment to some of the agency's critics, who had hoped that Ruckelshaus would win the administration's support for stronger environmental legislation and a national program to control acid rain.

Most of the laws that the EPA enforces are overdue for revision but have been mired in Congress for more than three years, and Ruckelshaus failed last year to win White House backing for a modest proposal to curb the sulfur emissions that cause acid rain.

The EPA administrator denied, however, that his resignation stemmed from frustration over administration policies. "I have relied on my stomach to tell me when to move," he said, adding with a grin, "I don't seem to be able to hold a job very long."

Ruckelshaus last resigned from a government job during the Watergate era, when he quit as deputy attorney general rather than carry out a White House order to fire special prosecutor Archibald Cox.

Ruckelshaus has not announced his plans. His resignation leaves open the question of how many of the agency's top officials, many of them handpicked by Ruckelshaus, also will depart within the next few months. Deputy Administrator Alvin Alm has made known his plans to leave on Jan. 5, the same day as Ruckelshaus.

One of those who will be staying is Lee M. Thomas, head of the hazardous-waste division, who was nominated at Ruckelshaus' suggestion as his successor and is expected to win Senate confirmation with ease.

Ruckelshaus praised Thomas as an honest and experienced administrator, counseled him to "cut these people loose and trust them" and offered one observation.

"You get two moments in the sun -- once when you come and once when you leave," he said. "Every day in between, it rains on you."