The man had reportedly been swimming in the All-American Canal on Saturday when he drowned.
The county Sheriff's Office dive team responded to the call this morning and helped remove the body from the water. The identity of the man was unknown.
Hayes said it was unclear to investigators whether the man was trying to cross the border illegally or was swimming in the canal for recreation.
The other death occurred Friday.
According to Border Patrol officials, someone in the Plaster City area reported a group of people walking near old Highway 80.
Border Patrol agents responded and apprehended the group of undocumented immigrants.
That group reported there was another group in the desert that looked dehydrated and in need of help.
Agents searched the area.
That group reportedly ended up on a train passing through the area.
A railroad worker spotted the group on the train, stopped it and then found a woman in the group had already died on the train.
The identity of the woman was unavailable this morning.
Border Patrol agents apprehended 10 illegal immigrants after a single-car accident west of El Centro.
According to a California Highway Patrol press release, one of the 10 individuals was driving a 1991 sedan with nine passengers and heading north on Forrester Road south of Ross Road about 1 a.m. Sunday.
The driver tried to turn onto a dirt canal but ended up driving into a dirt drainage ditch.
All occupants fled the scene.
Border Patrol agents apprehended all 10 individuals. One complained of back pain and was taken to El Centro Regional Medical Center.
A spokesman for the Border Patrol said the person taken to the hospital was released and turned over to the Mexican consulate.
The other nine were in custody and will be released pending an investigation.
Investigators had not established the identity of the driver.
Hayes said the three deaths, and others in recent weeks are signs the "busy season" for his office has started.
He said it likely will remain busy through the summer and into December as people cross illegally into the United States.
Staff Writer Darren Simon can be reached at 337-4082.