The Water Quality Program's mission is to protect and improve Oregon's water quality. Protecting Oregon's rivers, lakes, streams and groundwater quality keeps these waters safe for a multitude of beneficial uses such as drinking water, fish habitat, recreation and irrigation. This is accomplished by developing and implementing water quality standards and clean water plans, regulating sewage treatment systems and industrial dischargers, collecting and evaluating water quality data, providing grants and technical assistance to reduce non-point pollution sources, and providing loans to communities to build treatment facilities.

The program includes the Water Quality Division (at DEQ headquarters), water quality sections in three regions, and two monitoring sections at DEQ's laboratory.