One boater was given a £1,800 fine, which the government body called a “stark warning”.
The EA said every owner caught up in its December 2023 operation was traced and given ample opportunity to register their boats correctly.
Colin Chiverton, EA environment manager, said: “Our enforcement officers have no love, secret or otherwise, for unregistered boats on the Thames.
“They’re out all year long patrolling the river, checking valid registrations and taking action against those who cheat their fellow boaters.”
Mr Chiverton warned the agency would bring further offenders to court.
The EA said boat registration fees allowed it to manage and maintain more than 600 miles of inland waterways across England.
It likened the fee to excise duty for cars.