He joined others on a Kent fishing boat for the stunt directly outside the Houses of Parliament ahead of Prime Minister's Questions on Wednesday.
Earlier, prominent Brexiteer and Tory MP Jacob Rees-Mogg, who did not board the vessel, said he believed Theresa May had made a mistake on the deal, which will see Britain effectively remain in the European Union's Common Fisheries Policy until the end of 2020.
Speaking to reporters at Embankment Pier, Mr Rees-Mogg, who was asked if Mrs May had let down fishermen with the deal, said: "I think that it is a mistake."
On what Mrs May could tell the Commons to reassure them about the agreement, he said: "What can she say today? Well I think it's very important that the rules between our formal date of leaving and the end of the implementation period do not have an unfair effect on our fishing communities.
"And that relates to things like choke quotas, and there are proposals for changes that could be particularly damaging to the UK fishing community, and that's where we have to have the greatest concern. I would prefer it of course if we left properly on March 30 2019."
He said the protest was an effort to highlight the "plight" of fishing communities.
Mr Rees-Mogg added: "We hope that things will change. We need to ensure that we have a vibrant fishing community and we want to make sure that it survives to the end of the implementation period to benefit from our being free of the tyranny of the European Union."
Fishermen and many Brexiteer Tories are furious the UK will effectively remain subject to the EU's Common Fisheries Policy during the 21 month transition after Britain leaves in March 2019.
Ministers insist they have agreed "specific safeguards" with Brussels over the annual negotiations on fishing quotas in 2019.
But in the Commons yesterday a series of angry Tories rose to denounce the agreement hammered out between Brexit Secretary David Davis and the EU negotiator Michel Barnier.
Yorkshire MPs, including Hull MP Diana Johnson and Penistone MP Angela Smith, whose father was a deep sea fisherman in Grimsby, have also expressed their concerns.
In a sign of Government unease about the reaction, Theresa May met MPs with fishing ports in their seats in an attempt to explain their approach.
YP Letters: UK risks being a vassal state after BrexitPaul Butters, spokesman for the Best for Britain campaign group, said: "The Brexiteers are lost at sea with a stupid stunt like this. Today's comedy of errors is a metaphor for their Brexit plans.
“This was most embarrassing event to grace Westminster since the Leadsom for Leader march.
"The people who wanted Brexit are literally polluting the place with their never-ending complaint that it wasn't exactly what they wanted. They have had years to plan and the combined brain power of Rees Mogg and his motley crew came up with the idea of this stunt, circling round in the Thames unable to pick people up because they didn't have the necessary permissions.
"Taking back control from faceless bureaucrats maybe needs to start with Transport for London who run the pier they tried to dock at. All in all this was a fishing farce that made them all look ridiculous."
Meanwhile European Council president Donald Tusk has warned there is no guarantee EU leaders will accept the agreement covering the terms of Britain's withdrawal when they meet in Brussels this week.
Mr Tusk said on Tuesday that he still needs more time to consult with "some of the most concerned member states" ahead of their two-day summit starting on Thursday.
The leaders of the remaining 27 had been expected to rubber stamp the agreement - including the transitional arrangements - finalised in the Belgian capital on Monday.
But in his letter formally inviting them to the meeting, Mr Tusk said: "Whether all 27 member states can welcome this at the European Council remains open. I still need a couple more hours to consult with some of the most concerned member states."
Failure to to secure agreement on the terms of the UK's withdrawal would be a bitter setback for Mrs May, casting major doubt on her goal of getting broad agreement on Britain's future relationship with EU, including a free trade deal, by October.
Michael Gove admits Britain’s inability to take back control of fisheries on Brexit day is disappointingDowning Street insisted they had made "very good progress" in reaching agreement with the European commission on the transition.
The Prime Minister's official spokesman said: "The European Commission has been clear, as has the European Council, that getting a deal is in the interests of not only the UK but businesses and people across the EU."
Environment Secretary Michael Gove - a leading figure in the Leave campaign - has expressed his "disappointment" at the EU side's unwillingness to move on the issue.
Yorkshire representatives also voiced their concerns, including Halifax MP and shadow Fisheries Minister Holly Lynch, who told The Yorkshire Post: “The reality is he very personally committed a great deal to the hard and fast line that we were leaving the Common Fisheries Policy and taking back control from the get-go of leaving the European Union. He personally has misled people.
“He’s either been unable to deliver that in negotiations, which was never in his thinking up until now, or he’s not been honest about Government position and policy has been on this.”
Hull North MP Diana Johnson asked Mr Gove in the Commons: “The future of the fishing industry is a politically sensitive issue in Hull and Ukip have talked about a fishing fleet being re-established in Hull.
“But wasn’t one of the main promises made to the people of Hull that we would retain our territorial rights around fishing from day one and isn’t that a promise that’s been broken to the people of Hull?”
Penistone and Stocksbridge MP Angela Smith called for a guarantee that fish processing would not be sacrificed in exit talks. She said her father was a deep sea fisherman in Grimbsy, adding: “So I know it’s one of the hardest jobs in the world.”