Anthropogenic eutrophication and pollution of coastal waters requires careful monitoring of their “biological health”. This is often done by measuring stocks or rates of production. Monitoring primary productivity of coastal waters will lead to a better understanding of their basic functioning, including their capacity to support fish stocks or to develop harmful phytoplankton blooms. Charting primary production in coastal waters is, however, hampered by their optical complexity and heterogeneity, which prevents both accurate extrapolation of ship-based measurements and the retrieval of the distribution of photosynthetic pigments from satellite imagery. The Baltic Sea is extensively monitored with semi-autonomous water quality measurement systems (chlorophyll a, salinity, turbidity, temperature). These data can be used to improve the accuracy of remotely sensed parameters required to model primary production. In this project, ship-based measurements of phytoplankton photosynthetic activity are coupled to imagery from satellite platforms. An adapted Fast-repetition rate fluorometer with two excitation wavebands is deployed in the Baltic Sea, and novel satellite algorithms are developed for imagery of the Medium Resolution Imaging Spectrometer (MERIS). The potential of the data assimilation to obtain reliable regional coverage of phytoplankton primary production is evaluated, paying special attention to the interpretation of spatial variation of photosynthetic activity in and around phytoplankton blooms that develop massively in the Baltic Sea every Spring and Summer.