Bottom trawling represents nowadays one of the most severe anthropogenic disturbances at sea, and determines large impacts on benthic communities and processes. Bottom trawling determines also local sediment resuspension and the effects of the injection of large amounts of surface sediments into the water column have been repeatedly investigated. Few studies have assessed the consequences of sediment resuspension caused by bottom trawling on the quantity, biochemical composition and bioavailability of suspended organic particles and how these eventually rival those exerted by natural storms. To provide insights on this poorly addressed issue, we investigated concentrations and biochemical composition of total and enzymatically digestible pools of particulate organic matter (POM) in the Thermaikos Gulf (Mediterranean Sea) under calm sea conditions, during intensive trawling activities, and after a severe storm. We show here that sediment resuspension caused by trawling can cause large effects on POM quantity, biochemical composition and bioavailability. Both during trawling and after the storm, the relative importance of the carbohydrate pools increased (in the upper water column) and the total lipid concentrations decreased (in the intermediate and bottom layers) when compared to values measured during calm conditions. These results would suggest that bottom trawling could inject in the upper water column POM pools more refractory in nature (e.g., carbohydrates) than those present in calm or after-storm conditions. By contrast, we show also that the bioavailable fraction of biopolymeric C increased significantly during trawling in the upper water column of the shallowest stations and in the bottom water column layer of the deepest ones. These results provide evidence that bottom trawling can influence the overall trophic status of coastal waters, exerting effects similar or stronger than those caused by natural storms, though of variable amplitude depending on the water depth. Since bottom trawling is carried out worldwide and natural storms at sea can be frequent and intense, we claim for the need of assessing new adapting management strategies of bottom trawling in order to mitigate the synergistic impacts of anthropogenic and natural sediment resuspension on coastal biogeochemical cycles.