Oxygen and phosphorus dynamics and cyanobacterial blooms in the Baltic Sea are discussed using results from the Swedish Coastal and Ocean Biogeochemical model (SCOBI) coupled to the Rossby Centre Ocean model (RCO). The high-resolution circulation model is used to simulate the time period from 1902 to 1998 using reconstructed physical forcing and climatological nutrient loads of the late 20th century. The analysis of the results covers the last 30 years of the simulation period. The results emphasize the importance of internal phosphorus and oxygen dynamics, the variability of physical conditions and the natural long-term variability of phosphorus supplies from land on the phosphorus content in the Baltic Sea. These mechanisms play an important role on the variability of available surface layer phosphorus in late winter in the Baltic Sea. The content of cyanobacteria increases with the availability of phosphorus in the surface layers of the Baltic proper and the probability for large cyanobacteria blooms in the model is rapidly increased at higher concentrations of excess dissolved inorganic phosphorus in late winter. The natural increase of phosphorus supplies from land due to increased river runoff since the early 1970s may to a large degree explain the increased phosphorus content in the Baltic proper. Another significant fraction of the increase is explained by the release of phosphorus from increased anoxic areas during the period. These results refer to the long-term variability of the phosphorus cycle. In accordance to earlier publications is the short-term (i.e. interannual) variability of the phosphorus content in the Baltic proper mainly explained by oxygen dependent sediment fluxes. (c) 2008 Elsevier B.V. All rights reserved.