Free-living protists – single-celled eukaryotes – are an integral part of microbial food webs in aquatic environments. The aim of this thesis was to identify dominant protists and their functional roles in euphotic zones and deep pelagic redoxclines of the Baltic Sea. To balance the shortcomings of a single method approach, a combination of different techniques was applied: e.g., microscopy, gene sequencing, enrichment and cultivation. This work, in its methodological multiplicity, sheds considerable light on the diversity and functions of protist assemblages in the Baltic Sea.