Nutrients concentrations are declining since 1995 in the Wadden Sea, while phytoplankton biomass is increasing since 2005. A survey started in 2006 by the Lower Saxony Water Management, Coastal and Nature Protection Agency regularly monitors the abundance, biomass, and cell size of phytoplankton species in the East Frisian Wadden Sea. A total of 14 stations are sampled from a monthly to weekly frequency. Samples are taken at the surface using a bucket, and kept in 5L canisters with Lugol's iodine solution to be stored in the cold and dark until microscopic analysis. An inverted microscope was used to identify and analyze phytoplankton samples following Utermöhl (1958). The unaccepted or original names of species are given in the 'Species UID' variable, and the accepted identifications are given in the 'Species'. The data provides a detailed time series of phytoplankton species composition, biomass, and cell size diversity from 2020 to 2025 in the East Frisian Wadden Sea surface waters.