The short-term benthic response to an input of fresh organic matter was examined in vastly contrasting benthic environments (estuarine intertidal to deep-sea) using 13C-labeled diatoms as a tracer of labile carbon. Benthic processing was assessed in major compartments through 13C-enrichment in CO2, in bacteria-specific phospholipids and in fauna tissue. A rapid response was evident in all environments. Under warm bottom water (14–18°C), similar quantities of the added carbon were respired within 24 hours in shallow and deep-sea sediments. However, the speed and magnitude of respiration were strongly reduced under low bottom water temperature (4–6°C), both in a shallow and a deep-sea site. Rapid carbon respiration even in deep-sea sediments almost devoid of fauna highlights the key role of bacteria, the most ubiquitous benthic component, in this short-term respiration of fresh organic matter. However, when present, fauna rapidly ingest algal material, thereby increasing the amount of carbon processed and directly extending carbon flow pathways.