Purpose The presence of organic matter in cohesive sediment results in the formation of clay-organic flocs, which eventually impart complex rheological behavior including shear-thinning, viscoelasticity, thixotropy and two-step yielding to mud. In this study, the influence of microbial degradation of sediment organic matter on the rheological properties of mud samples, having similar densities, was examined. Materials and methods Mud samples were collected from three different locations in the Port of Hamburg, Germany, displaying varying organic matter content. The rheological analysis of fresh and degraded mud samples was performed with the help of several tests including stress ramp-up tests, amplitude sweep tests, frequency sweep tests, time-dependent tests, and structural recovery tests. Results and discussion The results showed a significant decrease in rheological properties including yield stresses, complex modulus, etc. for degraded mud samples as compared to the fresh mud samples. The slopes of the line, correlating the change (degraded − fresh) in the above-mentioned rheological properties as a function of the same rheological property of the fresh mud, varied within the range of −0.28 to −0.49. The structural recovery tests displayed a better recovery (i.e., stronger system) in mud after the pre-shearing step for the degraded mud samples as compared to the fresh mud samples. The effect of degradation time on the rheological properties of mud samples showed two critical time periods (3 days and 150 days) after which a significant change in rheological properties of mud samples was observed. Conclusions This study provided a useful understanding about the influence of organic matter degradation on the rheological properties of mud, which can be used to optimize sediment management strategies in ports and waterways.