Mrs Kalanick, 71, and her husband were found on the shore of Pine Flat Lake by the emergency services.
Fresno County Sheriff's Office said a preliminary investigation suggested their boat had struck a rock, with the Kalanicks both hurt in the collision.
A spokesman for Uber said the family had suffered "an unspeakable tragedy", adding that Mr Kalanick's father was in a "serious condition".
An investigation into the accident is ongoing, the sheriff's department said, with an autopsy due to be carried out on Sunday.
Mr Kalanick hit the headlines earlier this year when he was filmed swearing at one of his company's drivers.
He later said he was "ashamed" of his behaviour in an email to staff.
More about: #uber
