Yep, the SART (and other rivers-turned-flood-control-channels) is managed by the counties where it passes through their jurisdiction - San Bernardino, Riverside, Orange County. You'd be better off contacting the supervisors in the county where you live/have a concern, and it wouldn't hurt to send a letter of concern to the Southern California Association of Governments ('SCAG'), as they try and coordinate regional issues (especially applying for federal and state grant monies for projects like SART maintenance and/or rehab).
http://www.scag.ca.gov/Pages/default.aspx