In the present study, the composition and structure of the benthic protist community was investigated along a natural occuring salinity gradient. Samples were collected from both fresh- and saltwater locations in the meromictic lake Pollevann, as well from the lake's outlet, and the location where the creek meets the sea. The microbial community was investigated using the Illumina MiSeq sequencing approach. Both rDNA and rRNA were sequenced from sediment samples, in order to obtain an assessment of the metabolically active community, and to relate this to biophysicochemical factors measured in the respective environments.