Submarine groundwater discharge (SGD) is an often-overlooked component of the global hydrological cycle, significantly influencing coastal water quality. Although multiple models and studies exist for estimating SGD, large-scale assessments remain scarce, especially in areas experiencing intensive anthropogenic pressures, such as the Baltic Sea. These pressures include large coastal populations and land-based pollution, which contribute to the increased risk of local marine environments. Moreover, SGD can act as a critical pathway for transporting pollutants including nutrients into marine environments. However, the accurate regional scale estimation of SGD and its associated pollutant fluxes remains a challenge. To address this challenge, we develop a novel openly accessible, user-friendly, three-dimensional groundwater flow modelling tool specifically designed to quantify fresh SGD and related pollution in the Baltic region. The model integrates high-resolution catchment-based water budgets, including infiltration, precipitation, recharge, runoff, and evapotranspiration with digital elevation data, climate inputs, and aquifer properties. The model performance will be validated through catchment-scale water balances. Once validated in the Baltic Sea context, this model framework can be easily adapted to other regions, with comparable hydrogeological and climatic conditions. Planned future applications include examine how variations in climate, geology, and land use influence fresh SGD and the transport of both conventional and emerging pollutants. Future iterations of the model will incorporate density-dependent groundwater flow to address the effects of saltwater intrusion and saline SGD. By providing robust, spatially accurate estimates of SGD, this research offers a foundation for developing best management practices and targeted pollution mitigation strategies that consider local hydrogeological conditions. Keywords: Submarine Groundwater Discharge (SGD), Fresh SGD, Groundwater modelling, Pollution flux, Baltic Sea