These data sets were obtained in the context of the STW project “Sediment for salt marshes: physical and ecological aspects of a Mud Motor” with Project Number 13888, which is partly financed by The Netherlands Organisation for Scientific Research (NWO). The data set consists of 8 netcdf-files named cruiseXdeployment1/2.nc and 4 netcdf-files named filtration_cruiseX.nc. Each of the first 8 netcdf-files contains a 12.5h record of vertical profiles of current velocities, temperature, salinity, optical backscatter and the suspended particulate matter (SPM) concentrations derived from the optical backscatter using filtration samples. All data is interpolated to the same temporal and vertical grid. Measurements were carried out either near the port of Harlingen (deployment 1 on cruises 1-3, deployment 2 on cruise 4) or at the end of the Kimstergat channel (deployment 2 on cruise 1-3, deployment 1 on cruise 4). The files filtration_cruiseX.nc contain the raw data of the filtration: dry and