Despite a relatively small surface area on Earth, estuaries play a disproportionally important role in the global carbon cycle due to their relatively high primary production and rapid organic carbon processing. Estuarine sediments are highly efficient in preserving organic carbon and thus often rich in organic matter (OM), highlighting them as important reservoirs of global blue carbon. Currently, these habitats are facing intensified human disturbance, one of which is sediment dredging. To understand estuarine carbon dynamics and the impact of perturbations, insights into sediment OM sources, composition, and degradability is required. We characterized the sediment OM properties and oxidation rates in one of the world’s largest ports, the Port of Rotterdam, located in a major European estuary. Using a combination of OM source proxies and end-member modeling analysis, we quantified the contributions of marine (10–65 %), riverine (10–60 %), and terrestrial (10–65 %) OM inputs across the investigated transect, with salinity ranging from 32 (marine) to almost 0 (riverine). Incubating intact sediment cores from two contrasting sites (marine versus riverine) suggested that OM was more reactive in marine sediment than riverine sediment. Exposing wet bulk surface sediment to atmospheric oxygen in a bottle incubation experiment showed a 2.8–7.4 times increase of OM degradation rates, while the impact of OM source and composition maintained the observed differences in rates between sites. This shows that sediment perturbation and the reintroduction of oxygen can substantially boost OM degradation. By combining detailed quantitative characterization of estuarine OM properties with degradation rates under different environmental conditions, our results further our understanding of the factors that govern OM degradation rates in (perturbed) estuarine systems. Ultimately, this contributes to constraining the impact of human perturbation on OM cycling in estuaries and its role in the carbon cycle.