A long-term trophic development of three geographical transects—including a river mouth, an estuary, and an archipelago—were studied in the southern Finnish coast in the Baltic Sea. Each transect was studied to clarify how far off the coast the land-based nutrient sources (catchment factor, CF) had a decisive role in shaping the wintertime regimes of dissolved inorganic nitrogen and dissolved inorganic phosphorus and where the marine processes (marine factor, MF) start to play a major role. Generally, CF controlled the nutrient regime from the coast to the outer brink of the inner coastal area, after which MF started to dominate. The estuaries exhibited steep vertical nutrient gradients, above which the riverine input dominated the nutrient regime. The extent of the area where CF dominated the nutrient regime was therefore decisively dependent on estuarine stratification, i.e., whether the conclusions were drawn based on the surface layer data, including the riverine impact, or on the data beneath that layer, including the marine impact. This result deviates from the current consensus that the trophic regime of the sea is most directly assessed by the surface layer nutrient content. The estuarine nutrient regime is unrepresentative to that of a typical coastal water body due to the strong land-based impact on the estuary. Therefore, any generalization of the trophic condition of an estuary to represent areas farther off the coast should be done cautiously. The estuaries should also be defined as belonging to transitional waters according to the typology related to European Marine Legislation.