Kevin Murphy was suspended with pay last week as head of the animal control office in Adelanto, the Los Angeles Times reported. He faces up to six years in prison if convicted.
Another employee who has not been charged was also placed on administrative leave.
James Hill, a prosecutor in San Bernardino County, said Murphy allegedly drowned as many as 50 kittens between July and October last year.
Murphy received a Sheriff's Medal for Lifesaving in 2004 for rescuing a woman from a fire.
Kathy Williamson of the Victor Valley Animal Protective League in Apple Valley said she had a contract with the city to care for live cats and dispose of dead ones. She said animals euthanized at the shelter because they cannot be adopted are given a quick-acting drug.
"Years ago, before spaying and neutering, you'd hear stories of grandma out on the farm putting kittens in a gunnysack and throwing them in the river -- but not anymore," she said. "There are guidelines you must follow."