To quantify how fish farming modifies short-term benthic carbon cycling in fjord environments and the role of hydrodynamics in modifying effects on the benthos, we assessed benthic ecosystem structure and respiration and used isotope labeled algae as a tracer to quantify C flow over 48 h through macrofauna and bacteria in sediments collected from beneath fish farm sites in (1) high water-flow areas, (2) low water-flow areas, and (3) two appropriate control sites situated downstream from the farms. Bacterial biomass was significantly greater in sediments collected from the fish farm sites relative to the controls. This was also true for sediment oxygen consumption (SOC) rates averaged over each 48 h investigation, which were significantly correlated with total benthic (macrofauna and bacteria) biomass. Short-term C-uptake rates by macrofauna were elevated in both fish farm treatments compared with bacterial C uptake and were significantly higher in sediments from the low flow fish farm site relative to both controls. While SOC rates were significantly higher in experiments using sediments from the low flow fish farm site; faunal abundance, biomass uptake, C uptake, bacterial biomass, and metabolism in sediments from both fish farm treatments were not significantly different from one another. Fish farming can dramatically alter benthic ecosystem functioning, and significant effects can occur around fish farms irrespective of the water-flow regime the farms are moored in.