This study focuses on the integration of surface water and groundwater models to evaluate the quantity and quality of the surface water discharge and submarine groundwater discharge (SGD) to Puck Bay (Polish Baltic coast). The main goal was to investigate how the current land use and agricultural practices may affect groundwater recharge, SGD and the associated N-NO3 fluxes. The area is characterized by a complex groundwater system with two main aquifers formed in Quaternary fluvioglacial deposits (sand and gravel) separated by moraine tills. In the framework of the WaterPUCK project (www.waterpuck.pl) an integrated modelling approach has been developed, which couples the SWAT hydrologic model, MODFLOW-NWT groundwater flow model, and MT3DMS transport model. Model simulations showed significant spatial and time variability of groundwater recharge, SGD and the associated N-NO3 loads. However, there is no simple spatial relationship between recharge and nitrate load. Patterns of seasonal changes were distinguished, with maximum values of the SGD flux in late winter/early spring and minimum values in early autumn. Seasonal changes in SGD correspond approximately to seasonal changes in groundwater recharge. During the simulated period the relative differences between monthly averaged SGD fluxes in the shallow aquifer reach 120%, while in the deep aquifer they do not exceed 31%. A similar dependence is observed in the case of N-NO3 load to the Puck Bay, which is strongly controlled by the groundwater discharge variability. We will also present ongoing developments of the modelling platform, carried out in the framework of the EU Horizon project SOILPROM (grant 101156589, soilprom.eu). They include phosphorus transport model and improved description of water and nutrient movement through the deep vadose zone.