Boat owners at Pwllheli say they may demand their fees back from Gwynedd Council after claiming their moorings are being allowed to dry up.
They say a build-up of silt means moorings - which should guarantee boats stay afloat - are dry for up to five days a month.
Some are also angry at what they call a general lack of facilities.
A council spokesman said it was in the process of re-tendering all of the dredging works for the harbour.
Boat owner Ifor Hughes from Pwllheli, who pays £400 to moor his boat in the old dock, said: "This is a problem both in the marina (Hafan Pwllheli) and in the old dock area.
"It's got to the stage now that it is causing damage to some of the boats and people are talking about getting their mooring fees back."
David Hughes, who represents Pwllheli Chamber of Trade on the harbour committee said the problem had been building up for years.
"The dredger they (the council) bought was inadequate and not designed for tidal water, but since that was pensioned off there has been no dredging whatsoever," he added.
Mr Hughes said moorings were not cheap - with a pontoon mooring with no electricity would costing from £263.07 per metre (3.28ft).
A council spokesman said the local authority maintained Hafan Pwllheli to "the highest standard," including the toilet and shower facilities on site.
He said the marina had been awarded the Five Anchors Award, and a European Blue Flag Award.
He said the marina basin and inner harbour were dredged at least every three years to maintain an "adequate depth of water at most states of the tide".
"However, the depth of water within the harbour will inevitably decrease over time as a natural consequence of the sediment that is deposited within the harbour with each flood tide," he added.
He said the council was re-tendering all dredging works for Pwllheli harbour.