Just 50 licences are issued each year to collect cockles on the Dee estuary
Warm weather, barnacles and algae are to blame for a spate of cockle deaths in the Dee Estuary, Environment Agency Wales (EAW) has said.
Officials said the they did not think the problems would prevent the fishery opening as normal on 1 July.
Warm weather has claimed the highest number of cockles, with up to 20% on the densest part of the beds suffering "post-spawning heat-related stress".
The EAW said it would do its "utmost" to protect the beds.
Investigations began following concerns by fishermen earlier this year.
The annual cockle season sees around 3,000 tonnes of the shellfish collected from the estuary, worth up to an estimated £1m a year to the fishing industry.
The EAW said the heat-related deaths were a natural occurrence, not uncommon, which started in Mid May.
Also, on about 1% of the beds "there is a very unusual infestation of barnacles which appears to have caused a high mortality (75%) of cockles".
On about 1% of the Thurstaton bed there is a "large quantity of algae which appears to have caused high cockle mortalities, more than 90%".
Alan Winstone, of EAW, said: "At the moment, we do not think that this will have an effect on the cockle fishery opening as normal on 1 July.
"We will keep a close eye on the situation but the recent cooler weather will mean that the deaths should decline in time.
"We believe this fishery plays an important part in the local economy and, as regulators of the beds, we will do our utmost to protect it."