CAP is managed and operated by the Central Arizona Water Conservation District (CAWCD). CAWCD is a municipal corporation, also known as a public improvement district. This governmental entity was formed to repay the federal government for the reimbursable costs of construction and to operate, maintain, and manage CAP.

CAWCD employs more than 400 people who are responsible for system maintenance and operations, repayment obligations, and creating water resource management programs for Arizona. The day to day operations are managed by the General Manager and senior management team.

The General Manager reports to the 15-member CAWCD Board of Directors. Members of the Board of Directors are popularly elected from CAP's three-county service area including Maricopa, Pima, and Pinal counties and serve staggered six-year terms. The Board is responsible for establishing policy and usually meets twice a month.