Two months ago, the people who jigger the boxes on President Carter's government reorganization chart flashed the word that had been awaited since the famous campaign promise.

The promise was that a Carter administration would take the Army Corps of Engineers out of the Dambuilding business.

No more, the theory went, would the engineers be the rogue elephants of the public works jungle. Carter's reshaping of government would bring reason and care to water development and the environment.

At a December briefing, the reorganization team-left the environmental lobby with a clear impression that government water-resources programs soon would be housed together under the single roof of a new Department of Natural Resources.

The other shoe dropped yesterday with the president's formal proposal for creation of the new department. But water, although a natural resource, will not be a part of the department's mission.

Before the ink had dried on the White House news releases, the controversy was roaring. Vested interests and congressional jurisdictions were being stepped on right and left and they were howling in response.

The influential timber industry was indignant at the idea of moving the U.S. Forest Service out of the Department of Agriculture into the new department. House and Senate Agriculture committee members were fuming.

Congressional supporters of the National Oceanic and Atmospheric Administration were upset with the proposal to move that agency out of the Commerce Department. Commerce officals, who opposed the move early on, played the good-soldier role and publicly backed Carter.

Interior Secretary Cecil D. Andrus, who a month ago was saying in the inner circle that a new department wouldn't be much unless it covered water resources, told reporters that his new department (all of Interior would be in it) would do just fine without lakes, dams and other liquid matters.

Unless the House or Senate rejects the Carter reorganization, it could be a reality by early summer. A prognosis is difficult at best, but for now the flak is flying.

"He has retreated pretty far from taking the corps out of the dam-building business," said Brent Blackwelder of the Envoronmental Policy Center. "Why bother With a DNR if you are not going to include water? We think this is a breach of faith."

A similar feeling was expressed by Rep. Robert W. Edgar (D-Pa.), one of the House members who last year had joined with Carter and helped protect his veto of the public-works appropriation bill that funded some water projects the president opposed.

"It starts out to be a courageous stand, then things get muddled and the point men like myself, [Rep.] Butler Derrick [D-S.C.] and others are LEFT ALL ALONE. There should be some stroking, some consultation," Edgar said.

Why, in a span of less than three months, did Carter's reorganization team carry out a full reverse on the idea of putting the corps, the Soil Conservation Service and the Bureau of Reclamation under the same roof?

The best answer is politics, and an assessment sent to the president by Frank Moore, his congressional liaison chief. As Moore saw it, Congress would not abide any more tampering with the Corps of Engineers.

"That assessment was a major factor," a presidential aide said yesterday. "We had to decide on what was 'do-able,' and we knew that it would be a major fight in Congress if we included water under the DNR."

Moore's assessment included a check with members of the Public Works committees on Capitol Hill, where the sentiment toward changes in the water approach was, predictably, negative.

If Public Works was negative, so was Agriculture. Sen. Herman E. Talmadge (D-Ga.) and Rep. Thomas S. Foley (D-Wash.), chairmen of the respective committees, jointly warned Carter a month ago that hands should be kept off the Forest Service.

The ranking Republican on the House committee, Rep. William C. Wampler of Virginia, quickly reacted yesterday by introducing a bill to reverse Carter's idea and move everything into the Department of Agriculture.

Wampler's bill may not get very far, but it stood as a sort of symbol of the reaction when turf is invaded by alien forces and jurisdictions are threatened.

But in the view of another reorganization adviser at the White House, the targets have been chosen with care. "We looked for a hard one we could win, and we think it is this one, where we have an opportunity to control the process."

Which, of course, remains to be seen.