Ewen Beaton, 32, is still missing after the boat overturned in Loch Gairloch, near Ullapool, on Sunday afternoon.
His sons, Jamie, two, and five-year-old Ewen, died later that night after being rescued by helicopter from the water and airlifted to hospital.
A third child, Gracie Mackay, five, from Muir of Ord, near Inverness, died in the Royal Hospital for Sick Children in Glasgow yesterday afternoon.
Her 35-year-old father and eight-year-old sister, who were also in the boat, managed to swim 500m to the shore and raise the alarm.
The tragedy has shocked the local community. Muir of Ord councillor Graham MacKenzie said: "I know how terrible the community is feeling. It's a small community, but it's a very active one and very close-knit."
The former secondary school headteacher said: "The one thing I'm confident about is that the family will receive as much help and support as they want."
Fellow councillor Margaret Paterson said: "It's an unbelievable tragedy. My prayers are with the family and my heart goes out to them. There are no words that will comfort them at this time."
Northern Constabulary said the search for Mr Beaton, from Beauly near Inverness, began again this morning.
"A shoreline and land search recommenced today," a spokesman said.
His family said they were "utterly devastated" following the accident and the loss of the two young boys.
"We appreciate all that has and is being done by emergency services to find their adoring father, Ewen," relatives said in a statement.
Stornoway Coastguard was alerted to the incident at about 4.15pm on Sunday after Gracie's father and her sister, named locally as Garry Mackay and Callie, made it to the shoreline.
Peter Godding, sector manager for Stornoway Coastguard, said: "It's amazing really, she swam quite a long way in the sea, which is no mean feat.
"It's pretty incredible that she did survive.She would have given the police certain information which they didn't have.
"The girl that survived is very courageous and very resourceful to be able to complete a 500-metre swim to shore.
"That's no mean feat for an adult but she's achieved that and managed, in combination with the other adult, to raise the alarm. She's amazing."
When asked about the Canadian canoe the group had been in, he said: "They are quite cheap vessels to purchase and unfortunately it's quite difficult to maintain the stability if you stand up in them."
James Cameron, 34, who co-runs the Sands caravan and camping site in Gairloch, Wester Ross, said he and a friend found five-year-old Gracie.
He said: "I happened to be out in the boat yesterday when I heard there was an incident.
"We were just coming in and heard there was a girl missing, so we went out and actually found her.
"We found her face down, she was unconscious. She had her buoyancy aid on, it was keeping her afloat but it wasn't keeping her head out the water.
"We took her in and we did try our best to resuscitate her. The Coastguard helicopter then picked her up off the boat and took her away to Broadford Hospital."
Police would not comment on reports last night that the children were wearing life jackets but their fathers were not.