THE WAR OVER THE WETLANDS is flaring up again. The issue is whether Congress should cut back federal regulation of dredging and filling in the nation's wetlands and waterways.Groups representing farmers, loggers, developers, highway-builders and others want to end federal review of activities affecting small streams, uplands marshes and the like. Last year the House favored a cutback but the Senate, by a slim margin, stood firm. This winter the House passed another restrictive bill. Now the question is back before the Senate, which will be asked to choose - perhaps today - between a modified plan approved by the Environment and Public Works Committee, and the House approach, which Sen. Lloyd Bentsen (D-Tex.) and others are sponsoring. We favor the committee's plan.

The fight over little streams and out-of-the-way marshes may seem a bit obscure, but the areas at stake are hardly trivial. Wetlands are the nation's most productive natural hibitats. The serve as vital feeding and breeding grounds for wildlife, as sponges for flood control and as natural filters for polluted water. Moreover, damage to one minor tributary or swamp can affect a whole river system. The dumping of toxis spoil in a creek, for instance, can poison water supplies miles downstream.

Thus it makes sense to keep public review of dredging and filling just as extensive geographically as the potential problems are. Opponents have charged that such broad regulation is bound to be burdensome and meddlesome, but the program as it has evolved is very selective and sensitive. The Corps of Engineers' rules, issued July 19, make clear that the government will not concern itself with a broad range of routine farming, ranching, mining and forestry practices, and will approve a large assortment of minor maintenance and construction projects under general permits. This should preclude any horror stories about, for example, federal interference with the rebuilding of a mosquito ditch.

The Senate committee's proposal upholds this approach and also allows the states to take over the permit program if they wish. To us, this seems quite reasonable - and far more prudent than lifting all protection from many irreplaceable areas and allowing the dredgers and fillers to do whatever they want upstream.