Purpose Sediment organic matter (SOM) influences settling and thus the rheological behavior of suspended particles by enhancing flocculation or reducing surface charges by forming organo-mineral complexes that facilitate particle–particle interactions in consolidating sediments. It was, therefore, assumed that the microbial degradation of SOM and its spatio-temporal variability would affect sediment rheological properties and enhance port maintenance dredging and navigability of ports and waterways. Methods To investigate this effect, samples were taken at six locations along a transect of 30 river kilometers through the Port of Hamburg, Germany, during nine sampling campaigns within two years. The collected samples were divided into different layers based on the differences in visual consistency and strength. For analysis of SOM degradability, the samples were incubated in the laboratory for 250 days in glass bottles under aerobic and anaerobic conditions following the evolution of gas composition (CH4, CO2) and pressure in the bottle headspace over time. Yield stress was analyzed before and after the dissolved organic matter (DOM) decay using a rheometer with Couette geometry. Standard properties of solids and pore water were also analyzed. Results Shear strength decreased upon SOM decay under both anaerobic and aerobic conditions. Under anaerobic conditions, organic matter decay reduced static and fluidic yield stresses to an average of 74% and 79% of the fresh sample values. Consolidated layers at lower depths showed the highest absolute decrease in fluidic yield stress of up to –110 Pa due to a larger absolute amount of degradable organic matter in these layers in connection to higher bulk density. Pronounced spatial trends with higher changes in yield stress at upstream locations and lower yield stress changes at downstream locations coincided with a decreasing gradient of SOM degradability from upstream to downstream. Seasonal trends indicated that the investigation area is impacted by temporally changing factors. Conclusion The availability of easily degradable organic matter significantly affects sediment strength, especially under the anaerobic conditions, even when the mass loss of organic matter mass loss is small. Seasonal variability in yield stress changes upon SOM decay indicate that the site-specific responses were modulated by overarching seasonal effects impacting the entire investigation area. It was assumed that during an anaerobic decay, the formation of gas bubbles added an additional physical component to the effect of biological SOM decay.