As a part of its operating system, the district maintains an extensive gravity flow drainage system. The lateral drain system is laid out to provide a drainage outlet for each governmental subdivision of approximately 160 acres and, as such, the drains usually parallel the canals.

The district is obligated to provide its drains at sufficient depth - generally 6 to 10 feet deep - to accept tile drain discharge. Where the drain cannot be maintained at sufficient depth, a sump and pump are provided and maintained by the district. These drains are used to collect excess surface flow (tailwater) from agricultural fields, subsurface tile discharges and operational discharge from canals and laterals.

There are over 1,406 miles of surface drains that can be divided into three main areas: Alamo River System, New River System and drains that flow directly into the Salton Sea. Approximately 430 control structures are installed along the drainage system.