To illustrate their claims, the ACLU provides testimony by an inmate who says a deputy raped him.
"He just came in there and manhandled me, stripped me butt naked and sexually assaulted me and left me naked, bloodied and terrified," said inmate Frank Mendoza. "I remember just being left in a corner, shivering."
Mendoza alleges that there was no forensic evidence taken and it was not treated as a crime.
ACLU attorneys say Mendoza's case is one of a rampant pattern of human rights abuses by deputies. They also claim deputies failed to report use of force in several incidents.
"There is only one way that a notorious pattern of excessive force like this can go on for years in a prisoner jail: if top management decides to turn a blind eye," said Margaret Winter of the ACLU National Prison Project.
Baca could not be reached because he is out of town, but his spokesman denies rape and torture.
The spokesman said the sheriff met with ACLU representatives last week and took the unprecedented step of bringing in internal investigators to brief them.
The County Board of Supervisors recently appointed a jail commission to look into the alleged abuses and the sheriff now has his own task force to investigate.
"In the halls here, where justice and innocent until proven guilty has been talked about, when we talk about violent gang members on the street, that should certainly be afforded to deputy sheriffs who are risking their lives on a daily basis in the county jail as well," said sheriff's Cmmdr. James Hellmond.
ACLU representatives commend Baca for committing to reforms. However, they say they've been documenting violence in the jail system and making recommendations for change for four years and that a federal injunction is necessary to ensure them.