The effects of the hydraulic characteristics of a groundwater–lake interface on discharge and nitrate loading to a lake were investigated. The interface is defined as the zone separating the adjacent aquifer (10’s of m) and the lake bed (10’s of cm) itself. The study combines field data using several tracers (water, oxygen isotopes, and nitrate) and numerical modeling. The hydraulic head distribution, a nitrate plume and seepage rates were observed over a two-year period along a ∼100 m long transect reaching from an agricultural field into the lake. The groundwater–lake interface system was simulated with a 2D steady state flow and nitrate transport model (FEFLOW). The observations showed that discharge to the lake was doubled-peaked, with a peak discharge near the shore line followed by an almost (classical) exponential decrease, and a second peak further off-shore. The nitrate plume also extended 60–80 m off-shore. By calibrating the model to measured discharge and the outline of the nitrate plume it was demonstrated that; (1) the ratio of horizontal to vertical hydraulic conductivity (anisotropy) was very important and on the order of 50 and (2) the lake bed acted as a hydraulic barrier by having a much lower hydraulic conductivity than that of the relatively homogeneous aquifer. We suggest that the barrier is formed by an extensive plant cover that can trap finer materials and produce a surface colmation layer. The simulation results show that when a barrier is present the total groundwater discharge to the lake can be up to a factor of two lower and that approximately 50% of the nitrate bypasses the barrier. This proportion of the nitrate loading will therefore also bypass the plant cover and discharge directly to the lake off-shore potentially leading to algal blooms under N-limited conditions in the lake water column.