This thesis investigates a few important component processes for understanding and quantifying eutrophication in the Baltic Sea, that include characterization of nutrient loadings from land, water flow in the sea under changing climate conditions and transport of solutes originating from different locations along the coast. Furthermore, this study aims to improve our understanding on how processes from land (the nutrient loading conditions) and the sea (transport dynamics and water quality) couple to determine the fate of nutrients in the sea and the water quality in a selected localized coastal area, the Himmerfjärden Bay. Comprehensive data are compiled as a basis for numerical simulations. An open source tool for oceanographic studies FVCOM is used to simulate flow and transport processes in the Baltic Sea. Hydrodynamic simulations are verified in terms of temperature, salinity and water level for the year 2005. Results show that most of the investigated Swedish watersheds along the coastline are dominated by subsurface legacy sources, the loads of which are positively and linearly correlated with river discharges. Moreover, subsurface legacy sources are less likely to decrease over time compared with the current surface sources. The Baltic Sea has a stable flow structure considering flux directions between basins, while the flux magnitudes between basins are mainly determined by different wind conditions. The spreading patterns in the sea with solute released from different coastal areas are similar when the released amounts are comparable, even though different cases have different source input and water flow conditions. The overall spreading patterns in the sea are generally dominated by the total mass of released solute. Local transport dynamics and patterns around the coast differ greatly for different cases and are determined by the local flow conditions. Different water quality indicators are influenced by different land-based or sea-based measures for water quality improvement. The dry-cold hydro-climatic condition is the most favorable for improving the water quality and elevating the ecological status in the Himmerfjärden Bay. Based on this investigation, varying hydro-climatic factors impose important influence on the different component processes of nutrient loading from land to the sea. For example, the change of river discharges from land in the future would influence the total load into the sea from subsurface legacy sources, and finally influence the general spreading patterns of nutrients in the sea. The change of wind conditions would affect the flow and transport dynamics at local scale and flow fluxes magnitudes between marine basins at the sea scale. Change towards a dry-cold condition would be beneficial for the water quality and lead to improvement of coastal water quality, while the change towards a wet-warm condition will be generally unfavorable for improving the water quality. Clearly more comprehensive studies are needed based on the component processes considered in this thesis, for mapping water quality and eutrophication long-term trends in the Baltic Sea with confidence that is sufficient for effective mitigation measures and policies.