Groundwater in upland floodplains has an important function in regulating river flows and controlling the coupling of hillslope runoff with rivers, with complex interaction between surface waters and groundwaters throughout floodplain width and depth. Heterogeneity is a key feature of upland floodplain hydrogeology and influences catchment water flows, but it is difficult to characterise and therefore is often simplified or overlooked. An upland floodplain and adjacent hillslope in the Eddleston catchment, southern Scotland (UK), has been studied through detailed three-dimensional geological characterisation, the monitoring of ten carefully sited piezometers, and analysis of locally collected rainfall and river data. Lateral aquifer heterogeneity produces different patterns of groundwater level fluctuation across the floodplain. Much of the aquifer is strongly hydraulically connected to the river, with rapid groundwater level rise and recession over hours. Near the floodplain edge, however, the aquifer is more strongly coupled with subsurface hillslope inflows, facilitated by highly permeable solifluction deposits in the hillslope–floodplain transition zone. Here, groundwater level rise is slower but high heads can be maintained for weeks, sometimes with artesian conditions, with important implications for drainage and infrastructure development. Vertical heterogeneity in floodplain aquifer properties, to depths of at least 12 m, can create local aquifer compartmentalisation with upward hydraulic gradients, influencing groundwater mixing and hydrogeochemical evolution. Understanding the geological processes controlling aquifer heterogeneity, which are common to formerly glaciated valleys across northern latitudes, provides key insights into the hydrogeology and wider hydrological behaviour of upland floodplains.