ABSTRACTGroundwater discharge into lakes is an important component of the fluid and nutrient budgets, and a possible route for contaminant transport. However, groundwater flow beneath lakes is difficult to investigate due to the need for drilling deep boreholes. In 2012, a 2,000 m deep borehole was drilled in Lake Vättern, the second largest lake in Sweden. A continuous temperature profile was collected from the borehole. The geothermal gradient in the upper 180 m is highly non-linear, and not controlled by variability in the measured thermal properties of the sediments and rocks. The anomalous temperature profile is best explained by fluid flow into the borehole and subsequent vertical flow of warm waters towards the lake floor. Combining the temperature profile with stratigraphic information from drilling logs and seismic data, we find that fluid flow into the borehole occurs in glacial and glaciofluvial sediments deposited on top of a large sandstone aquifer (the Visingsö Group). The warm waters flowing through the glacial and glaciofluvial sediments are likely sourced from the underlying Visingsö Group sandstones. There is no evidence for substantial vertical migration of these waters through the overlying glacial and postglacial sediments. We speculate that they escape either along lake margins where overlying sediments become thinner, or along faults that are known to exist in the deeper basin.These results highlight an important hydraulic transport pathway between recognised regional aquifers and Lake Vättern. Further work is needed to evaluate the significance of groundwater discharge on the water and nutrient budget of the lake.