•Fully integrated groundwater model was used to simulate esker aquifer hydrology.•Locations of simulated GW–lake interaction agreed with airborne thermal image data.•Magnitude of simulated GW influx to lakes resembled stable isotope flux estimates.•Transient GW–lake interaction was revealed with fully integrated simulation method. Water resources management is moving towards integration, where groundwater (GW), surface water (SW) and related aquatic ecosystems are considered one management unit. Because of this paradigm shift, more information and new tools are needed to understand the ecologically relevant fluxes (water, heat, solutes) at the GW–SW interface. This study estimated the magnitude, temporal variability and spatial distribution of water fluxes at the GW–SW interface using a fully integrated hydrological modelling code (HydroGeoSphere). The model domain comprised a hydrologically complex esker aquifer in Northern Finland with interconnected lakes, streams and wetlands. The model was calibrated in steady state for soil hydraulic conductivity and anisotropy and it reproduced the hydraulic head and stream baseflow distribution throughout the aquifer in both transient and steady state modes. In a novel analysis, model outputs were compared with the locations and magnitude of GW discharge to lakes estimated using field techniques. Spatial occurrence of GW–lake interaction was interpreted from airborne thermal infrared imaging. The observed GW inflow locations coincided well with model nodes showing positive exchange flux between surface and subsurface domains. Order of magnitude of simulated GW inflow to lakes showed good agreement with flux values calculated with a stable water isotope technique. Finally, time series of GW inflow, extracted as model output, showed moderate annual variability and demonstrated different interannual inflow changes in seepage and drainage lakes of the aquifer. Overall, this study demonstrated the ability of a fully integrated numerical model to reproduce observed GW–SW exchange processes in a complex unconfined aquifer system. The model-based estimates obtained for GW influx magnitude and spatial distribution, along with information on GW quality can be used to estimate ecologically relevant fluxes in future water resources management.