Floodplains are often conceptualized as homogeneous sediment bodies which connect streams with their respective catchment and buffer agricultural inputs. This has led to a general bias within the hydrological community towards research on sites where the floodplain is a clear conduit for groundwater flow. In humid temperate regions of central Europe, floodplains have experienced rapid environmental changes since the last glaciation, yielding significant bedrock weathering and predominantly fine-grained, highly stratified hillslope and floodplain sediments. Such heterogeneous sedimentary architecture leads to conceptual ambiguities in the interpretation of the hydrogeological functioning of floodplains, thus raising the question: Do floodplains act as barriers or conduits to groundwater flow? This study analyzes the Ammer floodplain close to Tübingen in south-western Germany as a representative mid-section floodplain in a temperate climate where the regional bedrock-geology is dominated by mudstones. Geological, geophysical, and geochemical characterization and monitoring techniques were combined to shed light on the internal geological structure as a key control modulating the floodplain hydrology. Two partially separate groundwater systems were identified: a gravel body at the bottom of the Quaternary sediments and a Holocene confined tufaceous aquifer, separated by low-permeability clays. Despite flow being predominantly along-valley, sulfate concentrations in the floodplain aquifers showed evidence of a strong connection to the gypsum-bearing hillslope, particularly where tributary valley sediments are present (e.g., alluvial fans). Results from a floodplain water balance suggest the hillslope- and floodplain-aquifer material act as a barrier to hillslope groundwater recharge, where a large fraction may be bypassing the local floodplain groundwater system.