Millions of sprat and hundreds of mackerel are dying, trapped in Tralee's ship canal and basin close to the town centre, amid fears of a risk to public health.
Marine biologist Kevin Flannery said large shoals of silver sprat have been washing up around Tralee Bay within the past two weeks, chased by mackerel.
In recent days, the dead and trapped fish had crowded the lock gates of the canal at Blennerville.
While a sprat shoaling phenomenon is often observed on the western seaboard, it is unusual in Tralee Bay.
Mr Flannery, attached to Dingle Ocean World aquarium, yesterday met with county council engineers at the waterway and warned the sprat were "trapped" in the canal.
He said the flushing system in the three-mile canal would only operate if the gates were regularly opened.
Eels, junior ray fish and shrimp, resident in the canal between the town centre and Blennerville, were also dying due to overcrowding of the waterway.
"Literally millions of sprat and mackerel are in the canal," said Mr Flannery.
"These are high fat, oily fish and there will be a noxious smell," he warned.
The marine expert calling for the gates of the canal to be opened more regularly to flush out the water.
Meanwhile, the increased shoals of sprat and mackerel in the canal due to the fine weather of the past weeks, has led to a fishing bonanza for local anglers — with hundreds of people fishing off piers in the bay area.
The near three-mile long canal, constructed in the early 19th century was used to ferry goods from the major transatlantic and European port of Blennerville to merchants in Tralee town centre. It was dredged and restored in the 1990s and is now a major amenity used by local rowing clubs.
A towpath walkwaywas built along the canal, as part of the Dingle and Kerry Way.
Kerry County Council said engineers were meeting yesterday to find a resolution and to organise a clean up.