ABSTRACT: Finfish aquaculture is playing an increasing role in global food provision, with accompanying increases in benthic impacts under intensive pen production systems. Deposited faeces under and near fish pens affect the seafloor environment and biogeochemical functioning. To maintain healthy coastal environments, many fish farms operate by alternating input and fallowing periods to allow benthic coastal receiving environments to recover from excess organic matter inputs. Here we used flow-through annular flume mesocosms to simulate sustained organic matter inputs to the benthos with a subsequent fallowing period of no inputs. To quantify the effects of excess organic matter loading on benthic receiving environments, we carried out repeated closed-system flux-studies to quantify benthic carbon mineralisation processes, with a focus on benthic oxygen, inorganic and organic carbon, nitrogen, phosphate, and sulphide fluxes, and redox state throughout the input and recovery period. We found that recovery periods are input dependent, with parameters requiring longer fallowing periods to recover following larger inputs. While some benthic parameter fluxes, such as dissolved organic carbon, sulphide and ammonium returned to their pre-input state relatively rapidly (1 to 2 mo) following cessation of inputs, others such as sediment oxygen demand, ammonium and redox required longer (>7 mo) to recover. Our results suggest that in situations where the benthic macrofaunal community has been severely impaired, extended fallowing periods may be required in order to permit the biogeochemical composition of the seabed to return to a more natural state, with implications for farm consenting permits and planning and operational fallowing practices.