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A 15-year (1997–2012) time series of chlorophyll  (Chl ) in the Baltic Sea, based on merged multi-sensor satellite data was analysed. Several available Chl  algorithms were sea-truthed against the largest in situ publicly available Chl  data set ever used for calibration and validation over the Baltic region. To account for the known biogeochemical heterogeneity of the Baltic, matchups were calculated for three separate areas: (1)the Skagerrak and Kattegat, (2) the central Baltic, including the Baltic Proper and the gulfs of Riga and Finland, and (3) the Gulf of Bothnia. Similarly, within the operational context of the Copernicus Marine Environment Monitoring Service (CMEMS) the three areas were also considered as a whole in the analysis. In general, statistics showed low linearity. However, a bootstrapping-like assessment did provide the means for removing the bias from the satellite observations, which were then used to compute basin average time series. Resulting climatologies confirmed that the three regions display completely different Chl  seasonal dynamics. The Gulf of Bothnia displays a single Chl  peak during spring, whereas in the Skagerrak and Kattegat the dynamics are less regular and composed of highs and lows during winter, progressing towards a small bloom in spring and a minimum in summer. In the central Baltic, Chl  follows a dynamics of a mild spring bloom followed by a much stronger bloom in summer. Surface temperature data are able to explain a variable fraction of the intensity of the summer bloom in the central Baltic.