Jose Nunez, 47, had worked as a detention deputy with the Bexar County Sheriff’s Department for 10 years.
He was arrested early on Sunday morning after the girl’s mother sought help from a local fire department.
The Bexar sheriff called the case “heartbreaking, disturbing, disgusting and infuriating all at the same time”.
Sheriff Javier Salazar said at a press conference on Sunday that Mr Nunez had been placed on paid administrative leave pending an internal investigation.
Mr Nunez has been charged with super aggravated sexual assault, a charge applied when the victim is under six years old.
Sheriff Salazar said the suspect is “not worthy to be part of this agency”, adding that he took advantage of the mother’s immigration status to threaten her to keep quiet about the assaults.
He vowed to immediately “cut [him] out like cancer” from the police force.
The girl had been sexually abused several times going back months, or even years, the sheriff said, adding that there may be more victims.
The mother, who is originally from Guatemala, had sought help from a local firehouse after the girl cried out for help at around 03:00 local time on Sunday.
Investigators say the suspect blackmailed the mother by threatening to report her undocumented immigration status to federal officials.
He faces a minimum of 25 years in jail if convicted.
Immigrants should not fear coming forward to report crimes, Sheriff Salazar added.
He said that his department is “filling out paperwork” to ensure that the mother is treated as a witness, and given “protected status pending the outcome of this case”, which would allow her to remain in the US.