Estuaries are often used as transport ways to cities and harbours in the hinterland and have emerged as an important focus in coastal research. Mankind aspires to understand and control the complex hydro‐ and sediment dynamics in order to optimize the system due to social‐economic demands. In this process, river regulations (e.g. dredging activities) change the natural dynamics of the environment sustainably. This study provides new knowledge about near bed cohesive sediment dynamics as well as of fine cohesive sediment dynamics not only under ‘natural’ tidal flow but also under the influence of Water Injection Dredging (WID). In‐Situ Particle Size Distributions (ISPSDs) and Primary Particle Size Distributions (PPSDs) measured in the German Elbe and Weser estuaries indicate that the organic and inorganic Suspended Particulate Matter (SPM) is in a flocculated state. The substrate for the organic matter, which is needed for flocculation processes, is mainly transported from the seaside into the estuaries. Regional differences in PPSD have been observed in winter when the freshwater discharge is high and the extension of the Turbidity Maximum Zone (TMZ) is large. Individual sorting between the seaward and landward section as well as in the TMZ has not been observed in summer when the TMZ extension is small. Regional differences in the PPSD have no influence on the ISPSD. The latter is controlled primarily by the particle collision frequency powered by tidal forces and increased Suspended Sediment Concentrations (SSCs). Although, flocs break‐up due to shear stress with progressing tidal current they do not change their PPSD. Knowledge about floc size and composition is important to estimate settling velocities of the SPM. Increased particle settling can lead to enhanced near bed fine cohesive sediment concentrations. High resolution vertical sampling of near bed SPM in the Weser and Ems estuaries indicates that the widely accepted 3‐layer models, often used to describe vertical, cohesive sediment distribution is evidently incomplete. Sedimentological and rheological parameters, statistically proven by a cluster analysis, have shown that the intermediate fluid mud layer has to be subdivided in a low‐viscosity fluid mud layer (I) and highviscosity fluid mud layer (II). On the basis of a multi‐parameter analysis it was possible to define the exact SSC‐limits of both fluid mud types. The upper boundary of the fluid mud (I) is characterised by a strong SSC‐gradient (lutocline) which is detected with the low frequency channel of a parametric sediment echo sounder. The amplitude of the acoustic interface correlates with the SSC‐gradient sampled at the acoustic interface which had not been quantified before in literature. Decreasing SSC‐gradients with progressing tidal currents indicate an interfacial mixing but significant changes do not occur in areas of smooth bed morphology until one hour after slack water. Fluid mud (II) layers are suggested to represent recurrent, cohesive sediment accumulations which frequently have to be dredged in harbours and navigation channels. Over the last few decades the hydraulic WID technique has gained increased interest for the removal of mud shoals and subaqueous sand dunes in tidal controlled environments. Extensive hydroacoustical, optical and ground‐truthing data collected during WID in the brackishand freshwater reach of the Weser estuary shows that the crests of subaqueous sand dunes were exactly removed at the demanded height. Potential dredging effects are restricted to the approximate dredging site. Destruction of the internal sedimentstructure is limited to the upper decimetres and mobilized sandy sediments are accumulated on the dune slopes or in the adjacent troughs. Significant variations in the SSC or floc size are neither observed in the brackwater nor in the freshwater reach although acoustic interferences suggest increased turbulences over a distance of some hundreds of metres at the current lee‐side of the dredging device.