Due to stagnant or even increasing phytoplankton biomass in the Wadden Sea since 2005, the Lower Saxony Water Management, Coastal and Nature Protection Agency started a zooplankton survey in 2015, regularly monitoring the abundance, biomass, body size, and species in the East Frisian Wadden Sea. A total of 10 stations are sampled monthly. Samples are taken using an Hydrobios Apstein net, 150 µm mesh size, hauled from 10 meters deep to the surface at constant speed (0.67 m/s). The net has an opening of 40 cm in diameter, and is attached to a cone with a 17 cm wide opening. Samples are collected with three vertical hauls and stored in a 1L container mixed with borax-buffered formalin (5%). Samples are analyzed in accordance with the standard procedure DIN EN 17204:2020-09 to measure abundance, dry and wet weight, and taxonomic composition. Organisms were counted and identified up to the species (if possible) or genus level using a Bogorov-Chamber and a stereoscopic magnifier. 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 zooplankton species composition, biomass, and body size distribution from 2015 to 2025 in the East Frisian Wadden Sea.