CSDA is governed by a 18-member Board of Directors elected by mail ballots. The Board consists of three directors from each of the six regions throughout California. The Board meets bimonthly in Sacramento to guide the Association's legislative and member benefit programs.

Local chapters are independent groups of special districts formed to create local networks of special district leaders. Chapter functions and meeting schedules vary by location with some meeting only annually to elect LAFCo representatives and some meeting as often as monthly to transact business, share ideas, and engage in educational opportunities. Members of chapters are not required to be members of CSDA.