About 50 to 60 French boats took part in the protest, gathering their fleet off the Jersey port of St. Helier. They started the journey back towards France in the early afternoon.
Ahead of the event, the UK had sent two Royal Navy patrol boats to protect Jersey from a potential French blockade. The government said its vessels would remain in situ after the protest "to monitor the situation as a precautionary measure".
France's minister for European Affairs Clément Beaune said on Thursday morning that "these manoeuvres don't impress us".
The country has also dispatched two patrol vessels to the area.
"I have spoken with David Frost, the British minister responsible for relations with the European Union. Our desire is not to maintain tensions but to have a rapid and complete application of the agreement. Nothing but the agreement and the whole agreement," Beaune added.
The core of the dispute is over post-Brexit arrangements for the shared waters in the stretch between France and Jersey. The government of Jersey has the sole power to issue licences, and as of last week all fishing boats were required to have one to operate there.
The French government has said the new requirements for French fishermen are "null and avoid", accusing the Jersey government of failing to give proper advance notice to the European Commission.
Speaking to Parliament on Tuesday, French Minister for the Sea, Annick Girardin, alluded that France could take retaliatory measures, which could involve the "submarine cable transmission of electricity" that supplies the island from France.
Although close to the French coast, Jersey is a British Crown dependency, and the British government has branded the French threat unacceptable and disproportionate.