Interior Secretary James G. Watt, every environmentalist's bad guy, found himself eyeball to eyeball with the giant whooping crane yesterday. And Watt wasn't quite sure how he got into the showdown.

It all started the day Watt took office and wrote the nation's governors telling them that he was on their side, especially in the area of transferring federal lands to the states.

Almost all 50 governors replied, compiling a shopping list of what they wanted. Texas Gov. Bill Clements asked for a little island off Corpus Christi in the Gulf of Mexico.

The island, which Texas has been after since Richard M. Nixon was president, is named Matagorda. It's a wildlife refuge. It also is the wintering ground of the majestic whooping crane, which has struggled to expand its threatened population from 15 to 78 birds since the feds set aside its wintering grounds on Matagorda more than 40 years ago.

Watt wrote back to Clements, as he did to all the governors, thanking him for the recommendation, promising to get Interior Department officials together with state officials and stating once again that he was "inclined to transfer management responsibilities to states wherever possible."

In the same sentence, he added that "there are, as you know, matters of policy and law which must be reviewed before I can make this commitment."

It was, in government parlance, one of those "thanks-for-the-suggestion -and-I'll-take-a-look-at-it" letters. Cabinet secretaries send them routinely.

But Watt has become so controversial that even normal bureaucratic procedures excite suspicions. And nothing was more likely to excite suspicions -- and emotions -- than the fate of a bird that has struggled to increase its flock by fewer than two critters a year for four decades.

To the defense of the whooping crane leapt the Defenders of Wildlife, an environmentalist group that doesn't trust Watt's bureaucracy or his bureaucratic letters.

Giving away Matagorda "could seriously undermine the chances for survival of this bird," John W. Grandy, executive vice president of the group, wrote to Watt. Not only that, said Grandy, but it would have "severe implications" for brown pelicans, southern bald eagles, arctic peregrine falcons, American alligators and several kinds of sea turtles.

Letting Texas get the island, Grandy added, "would show a singular disregard for the public trust."

Wait a second, Watt's public spokesman, Doug Baldwin, said in despair. It was just a polite bureaucratic answer to a governor. The letter, Baldwin maintained, simply repeated a "general philosophical statement that we want to transfer federal lands to the states wherever possible" and plan to talk to them about it.

"Didn't they read the part about complying with policy and law?" Baldwin asked.

Then Grandy added the coup d'grace. Not only was Watt endangering the whooping crane, Grandy said as he leaked his and Watt's letters to the press, but Interior had a "hit list" of 21 other wildlife refuges that might be turned back to the states.

"Did he say we had a hit list?" Baldwin asked. "Oh, come on."

The "hit list" was there, all right. But it came after another little bureaucratic nicety that Cabinet secretaries follow. One of Watt's aides was testifying before the Senate Appropriations Committee when Sen. James A. McClure (R-Idaho), a Sagebrush rebel in favor of returning federal lands to the states, asked if Interior wasn't looking at "disestablishing" some wildlife refuges.

"I have not," testified the aide, F. Eugene Hester, an assistant director of the Fish and Wildlife Service. McClure then asked Hester to take a look and Interior hurriedly surveyed its regional offices, which dredged up 21 candidates in less than a week.

"That's standard procedure," said the beleaguered Baldwin. "What do they expect us to do when a member of the Appropriations Committee makes a request? It wasn't the secretary's idea. We didn't dream that one up. We've got enough troubles without a hit list of wildlife refuges."

Which all goes to prove that, in the bureaucratic maze, an interior secretary who has gone out of his way to aggravate both bureaucrats and environmentalists is going to hear a lot of whooping whether he planned it that way or not.