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Paddleboarders and kayakers say being made to pay £20 to use the River Fowey is an unfair 'tax' on the sport.
Fowey Harbour has introduced a new registration scheme to improve water safety and charge all those who use the river equally.
Harbour Master Paul Thomas admits "I do feel like the bad guy" but says in the summer the team are being called to help paddleboarders on an "almost on a daily basis."
The authority says there has always been a charge on vessels in the water but until now they had not made a direct plea for paddleboarders and kayakers to sign up.
Paul Thomas say: "Nobody wants to pay, and I understand that but it's only right and proper that they all pay a little bit towards running this place and keeping it safe for everybody."
Andrew Hall, an experienced paddleboarder of 30 years, set up a petition against the "unfair" charges.
"I would certainly support a national registration scheme but this piecemeal charging per waterway is unjustified, inequitable and it is, in my opinion, a slow growing cancer that is going to consume all the waterways in the Cornwall area and is going to remove significant numbers of people from the water."
After registering each vessel, people will be given a sticker to identify their boards or kayaks so they can be reunited if they become separated. They are also sent safety information about the River Fowey, weather conditions, and general paddleboarding advice.
Fowey Harbour also plans to fund a paddle safety officer with the income from the scheme.
However some users are not convinced this is the best way to teach beginners how to use the water safely.
Samantha Brock, a regular paddleboarder on the River Fowey, says her worries are around beginners "not knowing the right conditions to go out in, how to inflate their board properly, the importance of life jackets" and "those are bigger concerns rather than being able to identify paddleboards."
Fowey Harbourmaster Paul Thomas says at this time is not practical to share a registration scheme with other harbours because "there are some practical complications in terms of handling people's money and their personal data" but accepts it is something they "aspire" do do in the future.
96% of inland waterways in England do not need a license but tidal waterways are managed by harbour and port authorities. How much they charge and whether this is a levy on use of the water or a fee to use facilities varies from place to place.
Members of British Canoeing have permission to use 4500km of licensed inland waterways in England and membership has increased from 36,500 to over 92,000 members.
Ben Seale, Paddle manager at British Canoeing, said: "While Harbour Authorities can set their own charges, what we are keen to see is that any charges are fair and proportionate and do not create a barrier to people participating."
"Importantly we want to ensure people are paddling safely and we would support any authority in promoting messaging or advice.
"British Canoeing has been working very closely with the likes of the RNLI to get safety messaging out to the public", he added.