A permit system prohibiting point-source discharges of pollutants may not be effective as the sole method of implementing water quality control plans. The classic example of this occurs in the Sacramento-San Joaquin Delta where a major water quality problem is the intrusion of salt water from the San Francisco Bay. When flows from rivers feeding into the Delta are reduced, whether naturally or by upstream diversions, salt water from the bay intrudes into the Delta. High salinities can cause problems for agricultural, municipal and industrial diverters in the Delta; for fish, wildlife, and their habitat; and for water quality at the CVP and SWP pumps in the southern Delta.
The Porter-Cologne Water Quality Control Act requires SWRCB to "establish such water quality objectives. . . as in its judgment will ensure the reasonable protection of beneficial uses. . . ." Beneficial uses include domestic, municipal, agricultural and industrial supply; power generation; recreation, aesthetic enjoyment; navigation; and preservation and enhancement of fish, wildlife, and other aquatic resources or preserves. Establishing water quality objectives for the Delta and determining how to implement them is a major ongoing water management issue in California.