The Spanish man, who was in his late 50s and had been living in Ireland for several years, was found by his son in the water at the Town Pier at around 8pm.
It's understood that the man was seen alive at around 7pm when he headed back to his trawler for a rest and it's thought that he may have slipped when boarding the boat.
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The man's body has been removed to Cork University Hospital, where it will undergo a post-mortem later today.