The Swedish Meteorological and Hydrological Institute (SMHI) is developing an integrated biogeochemical model system for the Baltic Sea. It consists of three coupled models; a marine biogeochemical-hydrodynamical model (SCOBI), a continuous riverine nitrogen transport model (HBV-N) and an atmospheric transport and chemical model (MATCH). It is supplied with a tool for presentation and analysis. The SCOBI model is a coupled one-dimensional model with high vertical resolution. Horizontal variations are taken into account by dividing the area into smaller boxes. The model includes primary phytoplankton production, nitrogen fixation and secondary zooplankton production. Nitrogen load from land is obtained through the HBV-N model, which simulates organic and inorganic nitrogen separately in catchments. The model is based on the hydrological model HBV, and the subbasin runoff is simulated on a daily basis. The HBV-N model is calibrated and validated against measured concentrations and water flow in rivers. The atmospheric input of oxidised and reduced nitrogen is taken from the annual assessments carried out with the MATCH-Sweden modelling system. MATCH-Sweden combines model calculations, using an atmospheric transport and chemical model, with observations of air- and precipitation chemistry data to give a detailed mapping of concentrations and deposition of nitrogen compounds over Sweden. Supplemented with monitoring data for the specific area of interest, the integrated biogeochemical model system makes a useful tool for environmental protection analyses; e.g. for interpretation of monitoring data as well as creating scenarios for studies of effects in changes of the nutrient loads.