Gregory Rodriguez is accused of assaulting at least 22 female inmates.
He has also been charged with one count of bringing contraband into the prison.
Authorities from the facility began investigating Rodriguez last July.
Rodriguez retired from state service last August.
Madera County District Attorney Sally Moreno says so far, 13 of the victims have been identified.
"These allegations are in no way a reflection on what the vast majority of those people do every day," explained Moreno. "In fact, we hope by removing this guy, the other officers that are doing such good work every day are encouraged to continue to do that.
Rodriguez is currently in custody at the Madera County Jail.
He's expected to be arraigned later this week.
If convicted on all charges, Rodriguez faces more than 300 years in prison.