Rivera's vehicle, a black Mercedes G Wagon, was later found in the car park with her handbag inside.
The Ventura County Sheriff, who is manning the search operation, confirmed the search had resumed as the sun rose above the Topatopa Mountains.
The lake will be closed to the public as dive teams have been called in to help with the frantic search. No other details have yet been released by officials.
Ventura County Sheriff's Department Capt. Eric Buschow, told the LA Times Josey was "in good health" following the ordeal.
"The family is going through a very traumatic time right now," Capt. Buschow said, later telling NBC LA: "This is considered to be a horrible accident."
He said they were able to confirm Naya's identity after finding her wallet on-board the boat.
The actress recently posted a message on her social media accounts, eerily writing that "tomorrow is not promised" along with a selfie.
"No matter the year, circumstance, or strifes everyday you're alive is a blessing. make the most of today and every day you are given. tomorrow is not promised," the star posted to her 1.5 million Twitter followers last Friday.
Rivera was pictured out and about with her son in Los Feliz, California just last week, wearing a grey mask and matching cap and shirt as she ran errands with her little boy.
The mask included the message: "If you are reading this you are too close!"
Rivera's life took a turn in late 2017 after she was arrested on domestic battery in 2017 against her ex-husband, actor Ryan Dorsey, who is the father of her child.
Dorsey claimed that Rivera struck him in the head and face, and hours after the alleged incident, her emotional court appearance was caught on camera for the world to see.
The charge was dropped after Dorsey told prosecutors he didn't want to proceed.
Rivera had been arrested after an altercation during which she allegedly hit her husband at their West Virginia home. Law enforcement said at the time that alcohol was a factor in the incident.
E! reported that "Naya's friends and family (were) very concerned for her wellbeing" following the explosive incident.
The pair were married in 2014 but finalised their divorce in 2018 and share joint custody of their four-year-old son.
Glee has been plagued by controversy, heartbreak and scandal, earning it the title of the "Glee curse".
Glee's leading male Cory Monteith, who played Finn, died of a drug overdose in 2013 at the age of 31.
His co-star, Mark Salling, also another series favourite in the role of Puck, killed himself in January 2018. He was 35.
Salling, who Rivera briefly dated, was awaiting sentencing on child pornography charges at the time of his death.
