RCMP Cpl. Rob King says the three-year-old boy was in a car seat that his father had attached to the back of the ATV.
The child's medical condition and the extent of his injuries weren't released.
King says the father was driving Wednesday with a group of six other people on three quads near Hudson Bay when his machine rolled into the slough.
Members of the group rescued the boy, who was initially unresponsive, but managed to revive the child, who was later flown to hospital in Saskatoon.
King says it is too soon to say if the child's father will face any charges.
Note to readers: This is a corrected story. Previous version misspelled King'd first name