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Knowledge related to land-use management impacts on the Baltic Sea ecosystem is limited. The constant release of pollutants into water bodies has resulted in water quality degradation. Therefore, only the innovative approaches integrated with research will provide accurate solutions and methods for proper environment management and will enable understanding and prediction of the impacts of land-use in the Baltic Sea region. Modelling approaches have become essential to address water issues and to evaluate ecosystem management. There are many water quality models, but only a few work in the operational mode and only some of them can be used as an interactive tool for environmental management to assess the impact of pollution on water quality. This study presents a new approach for investigating the influence of pesticides and nutrient fluxes from agricultural holdings and land-use structures on coastal waters of the Baltic Sea. Called WaterPUCK, this method will enable calculation of the sufficient amount of fertilizers, investigation nutrients, and pesticide sources and model: the fate and distribution of nutrients and pesticides in the surface water and groundwater; loads of pollution to surface water and groundwater; fluxes of nutrients via submarine groundwater discharge (SGD) to the Baltic Sea coastal environment; the processes and mechanisms influencing the persistence of nutrients in the environment; and predict the changes in land use and climate change influence on the Bay of Puck ecosystem.