Operating as if the Florida Keys were foreign territory, the U.S. Border Patrol has set up a roadblock here that netted 13 undocumented aliens and up to 150 pounds of marijuana in one day.

The roadblock also aroused the ire of motorists who were backed up as much as 20 miles Sunday night while trying to get home from their weekend island getaways. Motorists pelted police cars with rocks and bottles, and there were reports of sporadic fistfights.

"Some of the drivers were so furious, the officers were afraid to leave the safety of their police cars," said Jane Brookes, chief operator at the Florida Highway Patrol's Miami station.

Business interests in the tourism-dependent Keys were angered by news that the Border Patrol plans to continue the operation indefinitely, but Bob Adams, chief of the Miami Border Patrol office, said the checkpoint would be running more smoothly by next Sunday's end-of-the-weekend crush.

"The roadblock is functioning as a national border," Adams said. "This is something we've wanted to do for a long time. We've finally got the manpower to do it." The Miami office of the U.S. Border Patrol has been beefed up through the Reagan administration's Task Force on South Florida Crime.