Health officials say the 9-year-old child apparently died of a rare form of meningitis caused by an amoeba associated with the warm freshwater lake.
The boy's father, Jim Ariola of Wyoming, Minnesota, says he is in shock and struggling to come to grips with the loss of his son, who died after swimming in Lily Lake in Stillwater last week.
State health experts say that is where the child likely contracted the severe brain infection.
The amoeba enters the body through the nose during swimming or diving.
The boy was flown to a Duluth hospital on Friday, where his condition worsened, and he was taken off life support Tuesday.
Minnesota had a similar confirmed case in 2010. That child also swam in Lily Lake, which is now closed.