The Sanitation Districts are a partnership of 24 independent special districts, governed by Boards of Directors consisting of the mayors of each city within the Districts and the Chair of the Board of Supervisors for county unincorporated territory. The 24 districts work cooperatively with one administrative staff, led by the Chief Engineer and General Manager, Assistant Chief Engineer and Assistant General Manager, and Deputy Assistant Chief Engineer.

The Sanitation Districts are organized into seven Departments, with specialized Sections in each Department. The Table of Organization identifies these Departments and Sections, as well as the structure of the agency.