This paper underscores the importance of spatially dense geophysical data sets for making informed decisions in water management strategies. Such decisions may require understanding how site-specific subsurface architecture -especially hydraulic connectivity -impacts the response of a shallow aquifer to anthropogenic hydrologic disturbances (e.g. over-pumping of a shallow aquifer). At a 0.2-km2 alluvial floodplain site characterized by thick clay over fine sand to gravel and shale bedrock in the subtropical, sub-humid belt of the Gulf Coast of the United States, we image an asymmetrically shaped, compartmentalized, sand-dominated channel-belt using electrical resistivity tomography and 31 time-domain electromagnetic soundings probing to depths of ∼40 m and ∼90 m, respectively. Lithological interpretation and a hydrological model are developed based on the geophysical data and nearby sediment cores, where the resistivity of the groundwater is 9.1 Ωm. In a modelling scenario wherein the compartmentalized sand channel-belt starts out dry (i.e. an over-pumped shallow aquifer), we simulate 26 weeks of infiltration due to flooding of the surface. Preferential filling of the channel-belt occurs through its sides rather than from above, generating a new understanding of the hydraulic connectivity around and into asymmetrically shaped, sand-dominated channel-belts. This insight can inform decisions about the optimal placement of shallow water wells in a heterogeneous alluvial floodplain aquifer system and also highlights the dangers of over-pumping.