Bustamante had been on paid administrative leave over allegations of sexual relations with subordinate employees.
The county received an anonymous letter that detailed the sexual allegations on Sept. 12 and placed Bustamante on leave.
Bustamante is also a Santa Ana city councilman.
Bustamante announced his resignation in a letter Tuesday:
"The allegations in the anonymous letters were unsubstantiated because they are not true, however, I have decided to never put my family or me through this horrible experience again, therefore I have decided to resign my position with the county and pursue a career in the private sector. I am very proud of my twelve years of distinguished county service and will miss working with my friends and colleagues at the county."