Bottom trawling represents a substantial anthropogenic disturbance, significantly disrupting seafloor integrity and altering oceanic carbon storage. In this study, we conducted a benthic trawling experiment on organic-rich muddy sediments in the Mecklenburger Bight, southern Baltic Sea, employing an otter trawl. Multiple trawl tracks were made to assess the temporal impact of bottom fishing on the benthic ecosystem over time scales ranging from days to weeks. Focus was on the wide area where the net footrope was dragged between the otter boards, rather than on much smaller area impacted by the trawl doors. This study constitutes the first comprehensive investigation to systematically monitor the effects of bottom trawling on benthic oxygen, carbon, alkalinity and nutrient fluxes using autonomous in situ lander measurements. Seafloor observations revealed a profound impact of trawling on seafloor morphology. Flux measurements, coupled with sediment data, indicated reductions in benthic fluxes of O<sub>2</sub>, dissolved inorganic carbon (DIC), total alkalinity (TA), and nutrients within trawled areas compared to control sites. Additionally, observed variations in organic carbon remineralization rates suggest that bottom trawling suppresses benthic respiration by disrupting key biogeochemical processes. Fluxes of O<sub>2</sub>, DIC, and TA had not returned to baseline levels by the conclusion of the 16-day observation period, indicating prolonged disturbance effects although the reduction in O<sub>2</sub> fluxes was more caused by decreasing bottom water O<sub>2</sub> levels over the study period. Despite substantial alterations to the benthic ecosystem, modeling suggests that the reduction in benthic DIC and TA fluxes exerts only a minor influence on CO<sub>2</sub> release to the atmosphere compared to the much larger impact of pyrite oxidation in resuspended sediment.