It is becoming increasingly clear that cleaning up after the weapons of war - whether or not they are used in combat - is a major environmental challenge. Some examples of the problem:
* At the Y-12 nuclear weapons manufacturing facility in Oak Ridge, Tenn., recently, it was confirmed that 700,000 pounds of mercury were - as Defense Department officials put it - ''lost to the environment.'' For 30 years effluent from the plant, stored in ponds, has been seeping into Bear Creek and East Poplar Creek.
* Waste chemicals were discovered in drinking-water wells at a community near the Cornhusker Army Ammunition Plant in Nebraska. The Army offered bottled water to nearby residents and is looking for a permanent solution.
* At the McClintic Wildlife Station in Point Pleasant, W. Va., several ponds were discovered to be contaminated with highly toxic wastes left over from on old TNT plant that operated during World War II.
* Under pressure from environmentalists, the US Navy recently decided not to scuttle old nuclear submarines at sea. But that still leaves the problem of how to permanently get rid of the radioactive material. By volume, military radioctive wastes are at least several times greater than that produced commercially.
Federal agencies have stepped up their efforts to improve the situation, and evidence that this is having a positive effect now can be seen. But officials also acknowledge that much remains to be done and that it will take years and billions of dollars before the job is completed.
''I can show a lot of horror stories,'' Air Force Maj. Gen. William W. Hoover told lawmakers during hearings on 1985 water and energy appropriations. ''I can also show you a lot of good-news stories, as we have corrected many of these problems thus far.''
Speaking of the nuclear weapons programs run by the Defense and Energy Departments, General Hoover said: ''We are not now imposing any immediate health or safety problems on the public. But we have problems to redress, or we can get into that situation.''
Between 40 and 50 Defense Department sites are on the US Environmental Protection Agency's ''Superfund National Priorities List'' for waste cleanup. And officials recently reported to Congress that as many as 400 sites on 200 military installations ''may eventually require some form of remedial action.''
Sometimes this is not the Pentagon's fault, as ''midnight dumpers'' can strike remote military sites just as they do private property. Several hundred gallons of PCBs were dumped at Fort Lewis, Wash., last November. This required the removal of 1,850 tons of contaminated soil at a cost of nearly $500,000.
But other environmental problems are clearly the result of deliberate decisions by government and military officials.
The Interior Department has identified more than 4 million acres of land containing unexploded ordnance, and the Defense Department owns about the same acreage contaminated with such bombs and other ordnance, according to Pentagon officials.
Robert Stone, deputy assistant secretary of defense, recently described one troubling legacy of earlier actions:
''There are numerous small military outposts in Alaska abandoned at the end of World War II and in the 1950s. Many of these sites are hazardous, unsafe, and unsightly. There are leaking tanks, drums, and barrels of oil and other chemicals at these sites. Some sites have PCB-filled transformers that have leaked or been vandalized. In other places, unexploded shells and bombs present a danger to people who may be unaware of the hazards involved.''
Pentagon and EPA officials last year signed a ''memorandum of understanding'' on how to implement the federal Superfund toxic waste cleanup law on military property.
The Energy Department has asked for $7.6 million in supplemental 1984 funds to clean up and stop toxic waste leaks (some of which are radioactive) at Oak Ridge's Y-12 nuclear weapons plant and wants another $21 million to continue the job next year. Energy Department officials also want an extra $37 million this year for pollution control efforts at the Savannah River plant. The state of South Carolina has ordered the plant to stop those activities that have been contaminating local groundwater.
The Defense Department this year will spend about $150 million on its environmental restoration program at 134 active and inactive military installations.
The Pentagon also has budgeted for 1984 $5 million in research to reduce hazardous-waste production, and defense officials plan to be recycling all their solvents by 1986.
''The biggest payoff will be in minimizing our future potential liability associated with hazardous-waste handling and, inevitably, mishandling,'' Assistant Defense Secretary Stone told senators earlier this month. ''If we don't generate it, we won't mishandle it, dispose of it, or pay to clean it up 20 years from now.''
''We also won't be subject to the unknown future costs associated with damages people may suffer when exposed to hazardous wastes in the environment,'' he added.
It is generally agreed that the need for preventive measures will become sharper if the steady buildup in nuclear and conventional weapons planned by the Reagan administration continues. This may be especially true with the proliferation of new atomic warheads for the variety of nuclear bombs, artillery shells, mines, and cruise and ballistic missiles now entering the US inventory.
Some radioactive material from older warheads is recycled.
But new material is needed as well, and this adds to the problem of disposing of radioactive materials resulting from warhead production.
According to the Energy Department, there now are nearly 2 million cubic meters of defense-related low-level radioactive wastes buried at several sites around the country. There also are 309,500 cubic meters of highly radioactive wastes stored in underground tanks in South Carolina, Idaho, and Washington State.
The Energy Department is building a new high-level radioactive-waste processing facility at Savannah River. This is expected to be completed by 1989, after which the solidified waste will be shipped to permanent underground repositories.
In a final environmental impact statement, the Navy announced this month that it would not be sinking old nuclear subs as a means of disposal. Environmentalists had feared that even with atomic reactors removed, the hulls would leak radioactivity.
Instead, Navy official said, the subs' nuclear engine rooms will be buried at Hanford, Wash., and Savannah River.
The Navy now has seven decommissioned nuclear submarines in storage and plans to retire about 100 over the next three decades.