Since 2001/2002, the correlation between North Atlantic Oscillation index and biological variables in the North Sea and Baltic Sea fails, which might be addressed to a global climate regime shift. To understand inter-annual and inter-decadal variability in environmental variables, a new multivariate index for the Baltic Sea is developed and presented here. The multivariate Baltic Sea Environmental (BSE) index is defined as the 1st principal component score of four z-transformed time series: the Arctic Oscillation index, the salinity between 120 and 200 m in the Gotland Sea, the integrated river runoff of all rivers draining into the Baltic Sea, and the relative vorticity of geostrophic wind over the Baltic Sea area. A statistical downscaling technique has been applied to project different climate indices to the sea surface temperature in the Gotland, to the Landsort gauge, and the sea ice extent. The new BSE index shows a better performance than all other climate indices and is equivalent to the Chen index for physical properties. An application of the new index to zooplankton time series from the central Baltic Sea (Latvian EEZ) shows an excellent skill in potential predictability of environmental time series.