California Drought Alleviation Act of 2008 - Directs the Secretary of the Interior: (1) within 30 days after the declaration of a drought emergency by the governor of California, to make a written determination as to the existence of a drought emergency for Central Valley Project and State Water Project service areas; and (2) upon determining such an emergency exists, to temporarily exempt operations of the C.W. "Bill" Jones and Harvey O. Banks Pumping Plants from prohibitions under the Endangered Species Act of 1973 (ESA) against taking endangered or threatened species or adversely modifying critical habitat until drought emergency conditions are alleviated. Authorizes the Secretary to include in any such determination reasonable and prudent measures for the protection of an endangered species or its critical habitat.
Authorizes the Secretary to enter into a cooperative agreement with California to support the establishment of a fish hatchery program to preserve and restore the species Hypomesus transpacificus (Delta Smelt) in the Sacramento-San Joaquin Delta. Requires the program to be designed to establish a sustainable population sufficient to warrant the species' removal from lists published under ESA and the State of California Endangered Species Act. Deems Hypomesus transpacificus maintained, cultured, introduced, or reintroduced to be members of any subspecies or population segment listed under ESA for purposes of determining whether such subspecies or population segment is a threatened or endangered species.