The data-set was obtained in the German North Sea with RB Otzum (ICBM) between the East Frisian Islands Spiekeroog and Langeoog on March 3rd 2020 and between the islands Wangerooge and Spiekeroog on March 4th 2020. Conductivity, temperature, pressure and oxygen concentration were measured with a Seabird CTD (type 19plusV2). Oxygen saturation, temperature, salinity, turbidity and concentrations of Chlorophyll a and CDOM at the surface were measured by a Ferry Box (type 4H Jena Engineering). Sediment samples were taken with a Van-Veen-Grapple and phytoplankton samples were trawled with a plankton net. The weather data were obtained from the Time Series Station Spiekeroog (ICBM). On both days sampling took place for half a tidal cycle from ebb current peak until the maximum of the flood current. Transects contained three stationary CTD profiles at the boundaries and at the center of appropriate inlet. To investigate the impact of the groin located at the Harle inlet, two transects were sampled in the northern area of the groin and four transects south of the groin. The CTD was veered with a speed of around 0.1 m/s while the boat was drifting with the current. The downcast profiles were binned to regular 0.25 m intervals. The timestamps of all data sets are given in UTC.