Microalgae are the major producers of biomass and organic compounds in the aquatic environment. Among them there are toxic species (mainly dinoflagellates) known to have the potential to form Harmful Algal Blooms, the so called HABs. HABs are occurring more often and at new locations. In general, knowledge about biogeographic distribution of harmful algae in the northern hemisphere is limited and patchy. During this project, we will study the seasonal dynamics of marine protists, with special emphasis on toxic algae in the North Sea. Samples will be taken from four geographical distinct locations in the German Bight and from the Orkney Islands. Protist community composition will be assessed by Illumina sequencing and a newly developed fully automated biosensor system. The latter allows for automated sampling and filtration of water samples and automated detection of selected toxic algal species, while the detection is based upon electro chemical quantification of RNA by sandwich hybridization. Here we show first results of calibrating the biosensor for selected toxic algae that are known to occur in the North Sea. Furthermore, we also show preliminary results of the characterization of protist communities from spring to autumn 2016 at four different observation locations in the North Sea via Illumina sequencing.