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Selected Baltic Sea watershed River Runoff (BSRR) events during 1970–2000 were used as predictor in Generalised Linear Mixed Models (GLIMMIX) for evidence of simultaneous changes/chain of events (including possible time lags) in some chemical, physical and biological variables in the Baltic and North Sea ecosystems. Our aim was to explore for climatic-based explanation for ecological regime shifts that were documented semi-simultaneously in both ecosystems. Certain similarities were identified in the North Sea and the Baltic Sea salinity, oxygen concentration, temperature and phyto- and zooplankton parameters. These findings suggest that BSRR events which originate in the Baltic Sea catchment area modify and contribute to large scale ecosystem changes not only in the Baltic Sea, but also in the adjacent parts of the North Sea. However, the Baltic Sea inter-annual and inter-decadal variabilities of physical and biological parameters are driven by direct atmospheric forcing, typically with a relatively short lag. In contrast, such changes in the North Sea are influenced by both local and direct atmospheric forcing, typically with a longer lag than in the Baltic, and a more regional, indirect forcing from changes in the North Atlantic. We suggest that this interactive system partially is behind large scale ecosystem regime shifts found in both Seas. During our study period two such shifts have been identified independently from us in a study earlier in the Southern and Central Baltic in 1980s and 1990s and a later one in 2001/2002 in the North Sea. As a post hoc test we compared the 0+ year class strength of the North Sea herring with BSRR intensity, and found evidence for higher herring production in high BSRR periods, which further corroborates the idea of a remote effect from the large watershed area of the Baltic. Regime shifts as well as their semi-synchronous appearance in two neighbouring sea areas could be identified. GLIMMIX models provide opportunities for determining and understanding the mechanisms behind marine ecosystem long-term and large-scale changes. Many studies have shown the importance of climatic factors (identified by the air pressure index, North Atlantic Oscillation) to the physical and biological changes over the North Atlantic. Our study enlarges the areal and temporal scope of these observations, and provides further support and explanation for climate as the pacemaker for marine ecological changes. [ABSTRACT FROM AUTHOR]