Concerns have been raised about the application of acoustic startle technology to a waterbike to protect seals from salmon in the river.
The new method, aimed at protecting spawning salmon, is being trialled in the River Dee in Aberdeenshire.
The Dee District Salmon Fisheries Board hopes it will help combat falling salmon numbers.
But a group formed to protect the seals said it was concerned that water skiing could cause the mammals to panic.
Salmon stocks are in a dramatic decline.
In the last 10 to 15 years, catch in the River Dee has dropped by about two-thirds.
Protecting valuable salmon stocks is big business – fishing on the Dee brings millions to the local economy each year.
But balancing this with the need to protect and conserve other wildlife in the river remains difficult.
Because it is illegal to kill or injure a seal, fishing boards are trying non-lethal methods.
Jamie Urquhart, conservation manager for the Dee District Salmon Fisheries Board, said water scooter patrols with the acoustic deterrent device were an attempt to lure the seals away from the river.
“It makes an annoying noise for seals,” he explained.
“It’s basically deterring the seals and keeping them away from the noise. We’re slowly pushing the seal downstream and out of the river.”
The device is tuned to a frequency that bothers the seals but not the fish.
Used on Dee before, but not attached to a water scooter.
At the Ythan Estuary in Newburgh, much has been done to protect the growing numbers of seals hunting on the riverbank.
Lee Watson of Ythan Seal Watch said his concern is the use of a water scooter itself, rather than a static acoustic deterrent device.
“Acoustic deterrent devices have a history of research,” he said.
However, he explained: “We have some concerns that this is a new technique that has not yet been approved or agreed upon.
“Seals are mammals and have a beating heart, which causes alarm and panic and can cause injury.
“We support the conservation of salmon, but there are many factors.”
The fisheries board insists that the seals follow a protocol to ensure they are not harmed.
Dr Lorraine Hawkins is the river manager.
He stressed that the water scooter itself is not a deterrent.
“It’s just one way we get the deterrent towards the seal,” he said.
“We developed this method in consultation with the seal mammals research unit, so they are seal experts and they advise us on how to do it so we make sure no harm is done to the seals.”
The project is being piloted at Dee until April.