Rivera, 33, went missing on Wednesday after going boating with her four-year-old son at Lake Piru. He was found alone and asleep on the boat.
Divers and teams using sonar equipment found the body earlier on Monday.
Rivera is best known for playing the cheerleader Santana Lopez in the hugely popular musical comedy TV series Glee.
At a news conference on the shore of the lake on Monday, Sheriff Bill Ayub of the Ventura County Sheriff Department said police were "confident" the body was that of Rivera.
He added that there was no indication of foul play or that she took her own life.
Rivera's son told police they had gone swimming but she never returned. After a massive search and rescue operation found no trace of Rivera, police moved to a "search and recovery operation".
That included using side-scanning sonar, divers, sniffer dogs, helicopters and remote-operated submarine vehicles equipped with cameras.
Sgt Kevin Donoghue, a spokesman for the police department, earlier told the BBC that they were "putting every available asset and resource" into the search.
He added that Rivera's son had seen his mother "disappear beneath the water".
"Rest sweet, Naya. What a force you were," Rivera's Glee co-star Jane Lynch wrote on Twitter. "Love and peace to your family."
Another Glee co-star, Josh Sussman, tweeted: "Naya, you will be missed so much."