The Center for Environmental Science, Advocacy & Reliability (CESAR, as in Chavez!) sounds like a great place to "bring scientific rigor to regulatory decisions undertaken pursuant to environmental statutes." They have the web address of bestscience.org after all!
Likewise, the California Water Institute at Fresno State sounds like it "provides education, research and analysis of policy issues involving water resources including water quality issues and integrated regional water management planning"
Both places recently hosted a talk on water flows, science and the Delta Smelt, but I think that it's more likely that they presented biased opinion than neutral scientific research.
Why? One big clue lies in the board of directors @ CESAR (CWI does not list its advisors), which has Jean Sagouspe, a politically-active farmer in the Westlands Water District (see this post on his request for favors for campaign contributions to Feinstein and this post on his $$ earnings due to a federal order to release water to Westlands). Another big clue? CWI's "Current Projects" all ended in 2005.
Bottom Line: They may call it "science," but I call it