Dynamics of an estuarine biotic community captured in high spatio-temporal resolution using metabarcoding

Estuaries and coasts are dynamic transition zones linking freshwater and marine environments and are characterized by sharp physicochemical gradients. These regions support key ecosystem functions but are challenging to study due to their spatial and temporal variability. Here we present a dataset characterizing microbial community composition and environmental parameters across the Warnow River estuary and adjacent Baltic Sea coast in unprecedented spatio-temporal resolution. Over the course of a year, we sampled fifteen sites along a ~30 km transect up to twice per week, generating 16S and 18S rRNA amplicon sequencing data, flow cytometry profiles, and measurements of temperature, salinity, chlorophyll a, nitrate, nitrite, ammonium and phosphate concentrations. Spanning the salinity gradient from freshwater to brackish environments, this dataset resolves short-term dynamics and fine-scale spatial variation in microbial communities within a human-impacted temperate estuary. It enables the investigation of microbial dynamics, community turnover, and biogeochemical responses to environmental change, offering a valuable resource for modeling microbial processes in complex, human-impacted aquatic systems.