WCCCA is governed by a Board of Commissioners (BOC), with one appointed representative from each participating jurisdiction. This board is responsible for appointing the Agency Director, setting service levels, approving the annual budget, conducting financial audits, and establishing personnel policies.

Additionally, a Chief Executive Officers (CEO) Board works to address ongoing operational matters, including policy updates, purchasing decisions, and labor negotiations. This board comprises the Chair of the Board of Commissioners, representatives from the two largest participating agencies, and two at-large members appointed by the Board.