Floodplain inundation is believed to be the dominant physical driver of an array of ecosystem patterns and processes in the Upper Mississippi River System (UMRS). Here, we present a time series of daily surface water inundation depths (in feet) for floodplain surfaces in the UMRS. The time series data are for the months of April through September for select years since 1940. These months were chosen because it approximates the period during which most biophysical processes such as vegetation metabolism and biogeochemical cycling are likely to be strongest across the longitudinal gradient of the UMRS. Data were generated without water surface elevations from the mid-pool gaging location at Blanchard Island due to missing data. Data were derived from a geospatial model of surface water inundation developed for the UMRS and described in Van Appledorn et al. (2021; doi: 10.1002/rra.3628). We excluded areas permanently wetted (aquatic areas), surfaces in agricultural production, roads, and developed areas. The data are intended for use in geospatial analyses of UMRS floodplain ecosystem patterns and processes.