The family of five toured the islands when their vessel toppled about one mile west of Michigan Island before 20:30, the authorities said Friday.
The father was identified as Erik D. Fryman, 39, and the mother as Cari A. Mews, 29, both Loyal, Wisconsin.
Fryman and two of the children were found dead in the water after the sheriff's office in Ashland County after midnight. Strong thunderstorms overnight disabled rescue operations. The body of the third child was recovered near the island at about 10 o'clock on Friday.
Mews, who had parted company with the rest of the group, was in the waters off Michigan Island shortly after 10pm. Thursday. She was taken to safety by the crew of the research vessel Kidi of the US Geological Survey.
Master Chief Alan Haraf of the Ninth Coast Guard District said the children are 3, 6 and 9 years old.
Haraf said the storms were still going down as the kayak went down, but there was an apparent shift in the weather as the family sailed between Stockton and Michigan Islands kayaks. All five members wore life-jackets as the kayak capsized.
"They started flooding with water and then they went under," Haraf told the newsstand.
Haraf said that the family lived in another part of Wisconsin but was known to make frequent visits to the Apostle Islands and had experience in kayaking.
The sheriff's office reported that the search began when Mews' sister called the authorities alerted text messages from the woman with the inscription "91
Police from La Pointe investigated and learned that the family had been vacationing on Madeline Island and had left earlier that day with the intention of kayaking on the lakeshore. The US Coast Guard, the Wisconsin Department of Natural Resources, the Bayfield Fire and Rescue, and the National Park Service were all involved in the search.
Haraf, who described the incident as "terrible", said that Fryman apparently tried with the three children, while Mews stayed at the place of capsizing with the ship and her supplies and sent the SMS to her sister.
Haraf said rescue workers were working around the clock, with relief at around 2 am He said the incident weighed heavily on Bayfield Coast Guard Commissioner and all other authorities involved.
"This crew really hurts," said Haraf. "They are really devastated, crews train to get the call and go out, they expect to help someone and bring them to safety, they are quite discouraged, in this case there are four members of the same family and if some of the crewmembers have children in the same age group, it hits them hard. "There are many heavy hearts in the ward."
The sheriff's offices and coroners in Ashland and Bayfield continue to investigate.