The Cache Creek Settling Basin (CCSB) is a 13.3 km2 leveed basin located at the terminal drainage of the Cache Creek watershed, immediately NE of the town of Woodland (Yolo County), California and approximately 18 km NW of Sacramento, California. The basin was constructed by the U.S. Army Corps of Engineers (completed in 1937 and modified in 1993) for the purpose of trapping suspended sediment transported from the upper Cache Creek watershed during high-flow events, thus preventing sediment from entering the Yolo Bypass, a larger downstream floodwater conveyance and agricultural zone. In addition to trapping suspended sediment, the CCSB also traps sediment-associated mercury (Hg), which is particularly elevated in the upper watershed, owing to natural Hg deposits and associated historic Hg mining areas. The CCSB is a multi-use area containing a number of habitat types that are typical of the California Central Valley region, including: open-water (stream, canal), riparian, floodplain (woody, non-woody), and agriculture (row crop fields) habitats. This dataset includes shallow surface sediment (top 0–2 cm interval) constituent concentration data (primarily) and microbial methylmercury production potential rate data (limited) collected between April 2010 and July 2017 from the above-noted habitats to assess spatial and temporal variations in sediment geochemistry and mercury speciation within the CCSB. The dataset is presented in two sections (child pages): one has the constituent concentration and microbial rate data, and the other includes results of habitat mapping that was conducted within the CCSB for the purpose of data analysis.