Coastal eutrophication is a major environmental issue worldwide. In the Baltic Sea, eutrophication affects both the coastal waters and the open sea. Various policy frameworks aim to hinder its progress but eutrophication-relevant water quality variables, such as chlorophyll-a concentrations, still exhibit opposite temporal trends in various Baltic Sea marine and coastal waters. In this study, we investigate the temporal-trend linkages of measured water quality variables and their various anthropogenic, climatic and hydrospheric drivers over the period 1990–2020 with focus on the Swedish coastal waters and related marine basins in the Baltic Sea. We find that it is necessary to distinguish more and less isolated coastal waters, based on their water exchanges with the open sea, to capture different coastal eutrophication dynamics. In less isolated coastal waters, eutrophication is primarily related to nitrogen concentrations, while it is more related to phosphorus concentrations in more isolated coastal waters. In the open sea, trends in eutrophication conditions correlate best with trends in climatic and hydrospheric drivers, like wind speed and water salinity, respectively. In the coastal waters, driver signals are more mixed, with considerable influences from anthropogenic land-based nutrient loads and sea-ice cover duration. Summer chlorophyll-a concentration in the open sea stands out as a main change driver of summer chlorophyll-a concentration in less isolated coastal waters. Overall, coastal waters are a melting pot of driver influences over various scales, from local land-based drivers to large-scale total catchment and open sea conditions. The latter in turn depend on long-term integration of pathway-dependent influences from the various coastal parts of the Baltic Sea and their land-based nutrient load drivers, combined with overarching climate conditions and internal feedback loops. As such, our results challenge any unidirectional local source-to-sea paradigm and emphasize a need for concerted local land-catchment and whole-sea measures for robust coastal eutrophication management. Available at: https://www.sciencedirect.com/science/article/pii/S0048969721014352?via%3Dihub