A study of potential sediment impacts on the Napa River was conducted by UC Berkeley and Stillwater Sciences to assess the validity of the State Water Resources Control Board's Section 303(d) (Clean Water Act) listing of the river as potentially impaired by sediment. The primary motivation for the listing is the concern that declines in native salmonid populations may be due to habitat degradation resulting from increased sedimentation in the Napa River. The phase-one study was funded by the State Water Quality Control Board and the State Coastal Conservancy as a precursor to implementation of a full Total Maximum Daily Load (TMDL) study. To identify habitat alterations that might impact population dynamics of analysis species, a conceptual reference model of historical conditions was developed for comparison with a concurrently developed model of current conditions. This allowed identification of changes that were likely to have caused the dramatic recent declines in steelhead, chinook salmon, and other analysis species. The models were developed using available information, interviews, air photo analysis, field visits and application of basic ecological and geomorphic principles to derive empirically based conclusions about ecosystem function. Digital information on topography, hydrology, geology, land use, and vegetation was assembled using a Geographic Information System (GIS). This preliminary assessment of current and historical conditions provided guidance for channel assessment and limiting factors analysis of habitat quality and quantity for salmonids.

Stillwater Sciences' approach included the use of a GIS as a tool to stratify the landscape into important land type categories based on important land use and physical characteristics. This stratification acts as a template to target field surveys to characterize the abundance and quality of important habitat features for the significant land types in the basin and allow reliable extrapolation to the basin as a whole. Habitat features that were evaluated include pool depth, spawning gravel area and permeability, undercut banks and streambed mobility, as well as flow patterns, temperature, habitat structure, and water quality. Information on these habitat features were characterized relative to the needs of critical life history stages of analysis species to determine the impact of habitat change on the population dynamics and abundance of species of interest.

As a follow up, CALFED selected for funding a project jointly conducted by Stillwater Sciences, the University of Florida and the University of California, Berkeley to collect high-resolution digital topographic data using light detection and ranging technology (LIDAR) to develop a high-resolution digital terrain model (DTM) for the Napa River Basin and begin testing the application of such high resolution data for watershed assessment, such as channel network characterization and slope stability modeling. The LIDAR approach has created a spatially explicit information database of sufficient resolution to allow for rapid yet comprehensive watershed analysis and restoration planning. Staff of Stillwater Sciences has extensive working knowledge and demonstrated expertise with the various tools and technologies used for this project. The project focused first on early aspects of the LIDAR processing. These include comparing first and last return surfaces, extracting a research-grade, bare-earth surface and comparing filtering methods and thresholds to maximize the capture of terrain features while removing artifacts intrinsic to the surface extraction process. A second phase of the project, once the bare-ground surface was extracted, included the testing and the development of methods for feature extraction, such as a stream network and reservoir-recognition. These were subsequently combined with various geologic layers to develop a sediment budget for the Napa basin.