RNLI lifeboats from Islay and Oban were sent to the scene along with a rescue helicopter from Prestwick.
The local MV Loch Buie CalMac ferry, which serves between Mull and Iona, also joined in assisting, as did two local boats from the area whose owners volunteered to help.
The coastguard said when rescuers arrived, the fishing vessel had become flooded with a “significant amount” of water.
The three crew were rescued by lifeboat and were being taken back to land on Friday afternoon.
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CalMac services between Fionnphort on Mull and Iona were suspended for a time while the ferry assisted the coastguard, but they later resumed.
An HM Coastguard spokesperson said: “We received a distress call from a vessel at 8.10am. There were three persons on board.
“The vessel was taking in a significant amount of water.
“The three persons were rescued and we are currently escorting them back to safe haven.”
