The Baltic Sea climate is analysed based upon long-term oceanographic measurements. The objective of the work is to study the natural variability of present day climate with focus on the freshwater budget. The results are designed to be used for validation of climate models and for discrimination of the significance of modelled climate change scenarios. Almost 100 yr of observations are used in the study, including data for river runoff, water exchange through the Danish Straits (as calculated from river runoff and from sea level data from the Kattegat), salinity data from the Baltic Sea and the Kattegat, and oxygen content in the deep Baltic Sea. The analyses illustrate that freshwater supply to the Baltic shows large variations on time scales up to several decades. The long-term variations in freshwater storage are closely correlated to accumulated changes in river runoff. This indicates strong positive feedback between the amount of outflowing surface water from the Baltic Sea and the salinity of the inflowing Kattegat water. One implication of the study is that climate control simulations must cover several decades, probably up to 100 yr in order to capture the natural variability of present day climate. Also, models designed to study climate change for the Baltic Sea probably need to start integrating from the present day.