Hundreds of thousands of little goldfish were swept to an uncertain fate in the muddy Monocacy River when flooding from Tropical Storm David engulfed their sheltered pools here at one of the country's largest fish hatcheries.

The goldfish, many of them fresh from the hatching pools at the Lilypons Water Gardens, were carried into this Western Maryland river when it crested about 10 feet above flood stage last night.

Though opinions varied on how well the flooded-out goldfish will fare in the muddy river, it was certain that the goldfish growers had suffered quite a loss.

Fish, according to George L. Thomas III, owner of the hatchery 10 miles south of Frederick, Md., cannot be insured against flooding.

When Thomas left his 300-acre hatchery yesterday afternoon, its grounds still were divided into hundreds of separate ponds, each containing a specific kind of goldfish. But late last night, the Monocacy rose over a 22-foot dike and about 50 separate ponds suddenly became one muddy lake.

"We built the dike up along the creek and river, and you think it's high enough, but each time it seems it would be better if it was a couple inches higher," said Thomas, as he looked over his flooded ponds today.

The hatchery was damaged by flooding twice earlier this year and was devastated by flooding from Tropical Storm Agnes in 1972, according to Thomas.

Thomas said he'll never be able to precisely calculate how many fish were lost, but sadly acknowledged "it easily could be" several hundred thousand.

While at the fisheries, the goldfish led pampered lives from the time they were hatched as fry, as Thomas describes them, "no bigger than a splinter in your finger."

Living in ponds sheltered from predatory fish, the goldfish are provided a choice of their favorite natural foods and the finest manmade fish cuisine containing dehydrated animal liver meal and wheat germ.

Just how well they will do now that they are in the wilds of the Monocacy, which flows into the Potomac, is a matter of debate.

"Their survival rate in the wilds like that is not too good," said Sally Thomas, the wife of Thomas' brother and business partner, Charles.

"It's like putting a tame animal into a foreign environment. If he's been in a zoo all his life, he may not make it."

But Thomas had more faith in his fish. "They'll do okay in the Monocacy, he said.

Asked how they'd fare if they reach the Potomac, as some are expected to do, Thomas smiled broadly and said, "Well, you people down in Washington say you're doing a fine job with the Potomac, that there'll soon be beaches there and swimming. So if it's good enough for people, I guess it's fine for fish."

But whatever the fish's fate in the wilds, the flood that swept them away from the hatchery could be considered a lucky break.

Many of the fisheries' customers, all over the East and Midwest, buy the little goldfish, who measure from 1 to 6 inches long, as "feeder fish."

Most would thus have ended their lives in tropical aquariums-- as dinner for some exotic fish.