A study on Lake Væng in Denmark demonstrates a high potential for loading of phosphorous via groundwater to seepage lakes. Groundwater discharges are displayed as an important source of phosphorous to a lake due to: (1) high concentrations in the aquifer just below the lake, and (2) the main flow paths through the aquifer–lakebed interface either being overland flow through a seepage face, or focused in zones with very high discharge rates. In-lake springs have measured discharge of up to 7.45 m3 per m2 of lakebed per day. These findings were based on seepage meter measurements at 18 locations, stable isotope (δ18O) analyses, temperature profiles and mapping of ice cover distribution. Groundwater–lake interaction was modelled with a 2D conceptual flow model (MODFLOW) with hydrogeology interpreted from catchment multi electrode profiling, on-lake ground-penetrating radar, well logging and borehole data. Discharge was found to be much focused and opposite to expected increase away from the shoreline. The average total phosphorus concentration in discharging groundwater sampled just beneath the lakebed was 0.162 mg TP/l and thereby well over freshwater ecological thresholds (0.043–0.612, median = 0.117 mg TP/l). The study illustrates a direct link between groundwater and lake chemistry