The federal government's war on the South Florida drug trafficking might have to come to a halt.

College students expecting a Pell grant on Sept. 1 might get $162 less than they had been counting on.

And hard-pressed communities waiting since last October for $160 million in economic development loans and loan guarantees may have to wait a little longer.

Those are among the fine-print consequences if President Reagan makes good on his threat to veto the supplemental appropriations bill that cleared a House-Senate conference committee last week. The White House has warned that the bill provides too much for domestic programs and not enough foreign military aid.

Two-fifths of the $14 billion measure would cover pay raises and salaries for federal employes and military personnel that have been approved over the past year. That money will continue to be paid, no matter what happens.

But the package also would provide funds for dozens of other programs, including:

* $148 million for education aid for economically disadvantaged children.

* $31.2 million to provide added security at U.S. embassies and consulates.

* $7.4 million for housing unsentenced prisoners.

* $4.75 million for the federal witness protection program and the services of expert witnesses.

* $5.8 million for pay raises for the faculty and other employes of Howard University.

* Authority for the District to pay $700,000 for increased costs associated with the new convention center.

* $9 million toward reconstruction of Wolf Trap.

* $3 million more for the Interior Department's inspector general to conduct audits of oil companies that pay royalties for oil and gas drilling on federal land.

The current debate on the measure, one House Appropriations Committee staff worker said, "epitomizes the problem with supplemental funding bills." He explained that it takes six to eight weeks to phase out a program, and if funding for those that the administration had wanted to terminate at the end of this fiscal year on Sept. 30 is not forthcoming immediately, the programs will become little more than a "bureaucratic machine intent on running itself out of business."

One example he cited is a program of community service employment for older Americans that Congress wants and the administration doesn't. The supplemental appropriations bill includes $211 million to continue funding various Labor Department contracts that run the program. If the money doesn't show up by mid-August, the agency will order the program to begin shutting down, which will stall it at least until the bill is finally passed or vetoed.

Another program tied up in the bill is the effort to control tuberculosis and immunize children against disease. Only $1.5 million is involved, but the Department of Health and Human Services needs it at the start of the school year.

Office of Management and Budget spokesman Edwin L. Dale Jr. emphasized that the current situation is different from the circumstances involving either the "urgent" supplemental appropriations bill earlier this summer when several agencies faced the prospect of extensive furloughs, or the continuing resolution last December when the federal government shut down for a day. Dale said the administration was trying not to alarm agency employes about "some mistaken type of forthcoming doom." CAPTION: Picture, More than $9 million is in the supplemental bill toward reconstruction of fire-gutted Wolf Trap. By James A. Parcell -- The Washington Post