Data Sources: Observations and GIS Data

Observational Data Sources (especially water quality & quantity)

California Dept of Water Resources CDEC California Data Exchange Center: river conditions, snowpack, precipitation, query tools. Also see 'other sources' link at http://cdec.water.ca.gov/sources.html

USGS Real-time Water Data for California

USGS Surface Water Data for California

Streamflow and some water quality parameters. Other links find groundwater and other data. Daily, Monthly and Annual data.
USGS Water-Quality Data for California very limited water quality data -- mostly discharge

GIS data sources

Seamless.usgs.gov USGS Seamless: for elevation, imagery, and other GIS data layers
National Hydrography Dataset National Hydrography Dataset: surface water features such as lakes, ponds, streams, rivers, springs and wells
USGS National Geologic Map Database   
USGS San Francisco Bay Water Quality Data