Bangor University scientists have joined forces with Conwy council to carry out research into the river Conwy's mussel beds.
Their work will focus on finding a possible source of microbial pollution that is affecting the mussels.
The numbers of shellfish allowed ashore has been restricted in recent years, and some beds closed.
The RSPB is also involved as pollution could impact birds in its Conwy sanctuary.
The study will involve collecting samples of the river water at various points, from Llanrwst to the mouth of the estuary, to build up a picture of possible pollutants entering the river.
"This is a great opportunity to combine the council's work with that of Bangor University to identify the potential cause of pollution," said Simon Cottrill, principal environment officer with Conwy Council.
Dr Shelagh Malham, from Bangor University's School of Ocean Sciences, said it was important to share all information available.
"We can agree future sampling patterns and locations, and gather all available evidence in order to make sure that the project provides value for money and that none of the work is duplicated," she added.
Dr Richard Quilliam, the researcher leading the project, said he can also see advantages for the fishermen.
He said the combining of resources would lead to recommendations that will "ultimately help the sustainability of the Conwy mussel fishermen's industry for many years to come".