Here, we report a dataset capturing the diversity and dynamics of the eukaryotic community at a 16 km stretch of the the Baltic Sea coast and the Warnow river estuary. From April 2022 to May 2023, we took surface water samples at fourteen sampling sites twice weekly and weekly samples at one additional site. After collecting the biomass in the sample on a 47 mm Durapore PVDF filter with a pore size of 0.22 µm, 18S rRNA gene amplicons were sequenced using the primers 5‘-CCAGCASCYGCGGTAATTCC-3‘ and 5‘-ACTTTCGTTCTTGATYRR-3‘ (Stoeck et al., 2010) targeting the V4 hypervariable region.