Seagrasses provide a variety of ecosystem services, including sediment stabilization, sediment accretion, improving water quality through trapping suspended sediments, and storing carbon and nutrients. Sharp declines in eelgrass (Zostera marina) abundance at South Slough have prompted efforts to understand eelgrass stressors in the estuary. Sediment characteristics including organic matter, carbon content, grain size distribution, bulk density, and porosity were investigated along with eelgrass metrics at several sites along the estuarine salinity gradient. These data were used to study the sediment characteristics of intertidal eelgrass beds in the South Slough estuary, how characteristics vary between sites along the salinity gradient, and to determine the relationship of sediment characteristics and eelgrass abundance. Results show that eelgrass was present at sites characterized by high percent sand and low percent silt/clay, low porosity and high bulk density, and low organic matter and carbon content. Eelgrass was absent from sites characterized by low percent sand and high percent silt/clay, high porosity and low bulk density, and high organic matter and carbon content. These results suggest that fine sediment may be one stressor contributing to changes in intertidal eelgrass distribution in the South Slough estuary. This study can help inform eelgrass restoration efforts in South Slough, especially regarding habitat suitability and site selection.