Sewer service provided by the City includes transportation to the City of San Diego's Point Loma treatment plant where it is treated and released offshore. The majority of the City's sewer costs are for the treatment by the City of San Diego. The sewer charges are calculated based on the water use at each property.

The City obtains information about water use from the water district providing the service to the property. Within the City, there are two water districts providing this service based on the location of the property; Helix Water District and Padre Dam Municipal Water District. The water district will notify the City when a water account for each property is activated or deactivated. The sewer charge will be based on the amount of the water used and the category of the use on the property.