We gathered benthic foraminiferal assemblages, organic matter and grain-size contents from surface samples along the transitional waters of the Elbe Estuary (North Sea). The data include 22 stations collected on July 2019 on board of the Research Vessel Ludwig Prandtl. Foraminiferal tables contain the counting of both living-stained and dead specimens. Organic matter contents were estimated by loss-on-ignition. Grain-size fractions (clay, silt and sand) were measured by means a Laser particle-size distribution analyser.