The present dataset contains 16S and 18S sequencing data (metabarcoding) from the Elbe estuary. The data collection was carried out as part of the DFG-funded project “Biota-mediated effects on carbon cycling in estuaries” within the RTG2530 (grant number 407270017). The aim was to analyze phytoplankton composition. Bulk water samples were taken at six different stations along the estuary in different seasons in 2021 and 2022. We provide the raw data as .fastq files, as well as metadata, processed data and a README file. The README file contains important information about methodological constraints. The 18S data, and part of the 16S data (picocyanobacteria) have been previously published (https://doi.org/10.1016/j.envres.2024.119126; https://doi.org/10.1002/pei3.70014).

Funding: Deutsche Forschungsgemeinschaft (DFG, German Research Foundation), grant number: 407270017 (RTG2530)