State Water Project water quality monitoring, by the Division of Operations and Maintenance, began in 1968 primarily to monitor eutrophication in the project facilities , and salinity for agricultural users. Over time the SWP water quality program expanded to emphasize parameters of concern for drinking water, recreation, and fish and wildlife purposes.

Today, chemical, physical and biological parameters are routinely monitored throughout the SWP (from the Feather River drainage in the north to Lake Perris in the south) including more than 40 sites and over 200 individual chemicals. Both discrete (grab) samples and continuous automated station data comprise a comprehensive water quality monitoring program. This extensive water quality monitoring program provides water quality data to: 1.) document special and temporal changes in SWP water quality; 2.) plan water treatment operational changes; 3.) identify and respond to pollution or other water quality episodes; 4.) compare SWP water quality to drinking water standards, Article 19 contractual requirements, or other criteria.