No matter the pronouncements in Washington, the Freedom Flotilla floated on today as rusty shrimp boats disgorged thousands of bedraggled refugees onto the docks of this sun-baked port.

President Carter's orders to half the disorganized exodus of Cubans from Mariel harbor seemed to make little difference in the refugee flow, but this was not necessarily an act of defiance against the president. Some vessels were on the water at the time of Carter's announcement, and there were reports that boats in Mariel were being forced by Cuban soldiers to take on refugees for the return trip here.

The major effect today of Carter's new policy was to add to the paperwork of harried U.S. customs officials.

Customs agents Wednesday night and today slapped large seizure notices on more than 70 vessels, but most of the boats were allowed to sail back to their home ports in southern Florida.Out-of-town vessels docked in Key West while their captains sought hearings.

There was no indication that President Fidel Castro would accept Carter's plan to have U.S. officials screen refugees in Cuba and transport them here on U.S. government boats or planes. r

Despite assurances in a Cuban Communist Party newspaper that the U.S. boats would be allowed to return freely to Florida, U.S. Coast Guard officials here said a radio report from a boat in Mariel this morning indicated that the boats would not be allowed to return without refugees on board, as Carter has ordered.

"The captain of the Tarasato told the [Coast Guard cutter] Dallas that all boats departing Mariel were being forced to take refugees on board," said one Coast Guardsman.

The Coast Guard began broadcasting regular warnings Wednesday night, ording Mariel-bound vessels to turn back. But few boats were leaving for Cuba anyway because Cuban Americans are discouraged by reports that Castro is loading up boats with political prisoners and Peruvian Embassy refugees, rather than the relatives that Cuban Americans seek to rescue.

So far, 841 boats with refugees have docked here, while 512 boats have returned empty after their owners ran out of food, money and patience in Mariel.

In Washington, Treasury Department officials announced late this afternoon that they are adding another weapon to the administration's enforcement arsenal -- the threat of $50,000 fines and 10 years imprisonment for those who violate the ban on bringing in Cubans illegally.

Richard Davis, assistant secretary for enforcement at Treasury, said the new amendments to the Cuban Asset Control Regulations were designed to provide additional authority to seize boats and in serious cases to impose the heavy criminal sanctions.

State Department officials, meanwhile, said they were not surprised at Castro's apparent initial refusal to cooperate. But they held out hope that strong law enforcement efforts and a willingness of the Cuban Americans to stop the flotilla for awhile would give the Carter administration time to increase the pressure on Castro for a more orderly arrangement.

Officials admitted, however, that the international negotiating team formed in Costa Rica last week so far has failed to make any headway in dealing with Castro. That goal was damaged, officials acknowledged, when some Latin American countries with cordial relations with Castro refused to be part of the negotiating team.

"They were concerned they'd be getting in the middle of something between the United States and Cuba that might spoil their relationship," one said.

If there is no change of position by Castro in a week or so, U.S. strategy is to have another meeting of the Costa Rica conference to increase pressure on Cuba, one official said.

Sen. Richard Stone (D-Fla.) said today that he thought it would take a day or two to see if the law enforcement effort has credibility.

"The early response from Cuban exile leaders in Miami is more compliance with the president's request than they expected. That is shown by the long lines at the family registration center."

More than 7,000 persons were lined up by mid-morning today to give federal officials the names of close relatives for the proposed U.S. airlift, a State Department official said.

Raul Masvidal, chairman and president of Biscayne Bank of Miami, one of the Cuban leaders briefed Wednesday by a White House official, said today that the Cuban-American community felt "confused by Carter's latest flip-flop on this issue. We're pretty much willing to go along with the president for now. But many feel it's totally unrealistic to think Castro is going to cooperate. We seem to be playing right into his hands again."

He added that anyone trying to sound out opinion in the Cuban community in Florida would find 25 answers from as many people.

In Key West, on the docks of the abandoned Navy base now converted to a refugee center, Nikolas Severdija, 42, lounged in bathing trunks on his 38-foot boat, Minegra. Severdija had just scurried in a cargo of 40 refugees and a bright red seizure notice glinted on his cabin door.

But Severdija said he was not concerned. The notice "is just to scare people off so they won't go to Cuba anymore," he said. "I fugure it will be taken off without any problem."

Severdija, like many of the captains arriving here, was confused by the mini-bureaucracy set up at dockside. "I went from customs to immigration to Coast Guard," he said. "I have a bunch of papers but I didn't read them. I don't worry very much about them."

Obligingly, Severdija fetched the papers from his cabin. The first was a seizure notice from the U.S. Customs Bureau, but Severdija said customs officials told him he could sail his boat home to Miami when he wished.

The second paper was a "Notice of Intention to Fine" from the U.S. Immigration and Naturalization Service declaring, "It appears that a breach of the law has occurred. You transported Cuban nationals to the U.S. without visas. You are granted 30 days to file a written dissent."

The third paper was a subpoena from the U.S. Coast Guard to appear Friday to testify at the Key West Coast Guard station, presumably for an alleged violation of marine safety laws.

While the papers might seem threatening on the surface, many persons here do not believe that immigration service fines will be imposed. Coast Guard subpoenas also are believed unlikely to result in prosecution since boat owners claim Cuban soldiers forced them to overload their vessels.

"Its better catching Cubans than catching shrimp," said Jack Hersey, a Tarpon Springs fisherman whose shrimp boat was chartered by 13 Cuban Americans for the trip to Mariel. Hersey, who sees the flotilla as an economic godsend for hard-up fishermen, scoffed at the notion that the government might levey fines against boat owners of $1,000 per refugee brought here.

"If they fine us, they'll end up with a lot of boats on their hands, because we can't afford to pay," he said. "They'd have to put me in jail and feed me for the rest of my life."

More than 46,000 Cubans have arrived here in the last three weeks. About 1,200 boats remained in Mariel today waiting to pick up relatives of Cuban Americans. Many Cuban Americans here seem to be taking a wait-and-see attitude before launching more boats toward Mariel.

"We were getting ready to go out again," said Ray Reimberto Cordero, who brought a boatload of refugees from Mariel last week. "But we heard the government is sending ships so they can come more safely."

If Carter's plan doesn't work, Cordero said, he won't hesitate to return to Mariel to pick up his mother.

Meanwhile, more than 10,000 Cuban-Americans stampeded the Opa-Locka Airport in Miami. Federal officials were setting up an office at the airport to receive applications for the proposed government-sponsored sealift or airlift.