In semi-enclosed seas, eutrophication may affect both the coastal waters and the whole sea. We develop and test a modelling approach that can account for nutrient loads from land as well as for influences and feedbacks on water quality across the scales of a whole semi-enclosed sea and its coastal zones. We test its applicability in the example cases of the Baltic Sea and one of its local archipelagos, the Archipelago Sea. For the Baltic Sea scale, model validation shows good representation of surface water quality dynamics and a generally moderate model performance for deeper waters. For the Archipelago Sea, management scenario simulations show that successful sea measures may have the most important effects on coastal water quality. This highlights the need to consistently account for whole-sea water-quality dynamics and management effects, in addition to effects of land drivers, in modelling for characterisation and management of local water quality.