Authorities said the charges against Thomas Lopez stem from a 2007 incident involving a female student.
Lopez, 36, works as a student specialist at Steele Middle School. He is also a former varsity baseball coach at Muskegon High School.
Superintendent Jon Felske said a letter was to be sent home to parents on Wednesday.
Lopez has been with the district for 10 years. He is being held without bond at the Muskegon County Jail.