Historical and recent remote sensing data can be used to address temporal and spatial relationships between upland land cover and downstream vegetation response at the watershed scale. This is demonstrated for sub-watersheds draining into Elkhorn Slough, California, where salt marsh habitat has diminished because of the formation of sediment fans that support woody riparian vegetation. Multiple regression models were used to examine which land cover variables and physical properties of the watershed most influenced sediment fan size within 23 sub-watersheds (1.4 ha to 200 ha). Model explanatory power increased (adjusted R(2) = 0.94 vs. 0.75) among large sub-watersheds (>10 ha) and historical watershed variables, such as average farmland slope, flowpath slope, and flowpath distance between farmland and marsh, were significant. It was also possible to explain the increase in riparian vegetation by historical watershed variables for the larger sub-watersheds. Sub-watershed area is the overriding physical characteristic influencing the extent of sedimentation in a salt marsh, while percent cover of agricultural land use is the most influential land cover variable. The results also reveal that salt marsh recovery depends on relative cover of different land use classes in the watershed, with greater chances of recovery associated with less intensive agriculture. This research reveals a potential delay between watershed impacts and wetland response that can be best revealed when conducting multi-temporal analyses on larger watersheds.