To the best of our knowledge, the understanding of benthic metabolism of coastal sedimentary areas is still limited due to the complexity of determining their true in situ dynamics over large spatial and temporal scales. Multidisciplinary methodological approaches are then necessary to increase our comprehension of factors controlling benthic processes and fluxes. An aquatic Eddy Covariance (EC) system and Benthic Chambers (BC) were simultaneously deployed during the winter of 2013 in the Bay of Brest within a Maerl bed and a bare mudflat to quantify and compare exchange at the sediment-water interface. Environmental abiotic parameters (i.e., light, temperature, salinity, current velocity and water depth) were additionally monitored to better understand the mechanisms driving benthic exchange. At both sites, EC measurements showed short-term variations (i.e. 15 min) in benthic fluxes according to environmental conditions. At the Maerl station, EC fluxes ranged from -21.0 mmol m−2 d−1 to 71.3 mmol m−2 d−1 and averaged 22.0 ± 32.7 mmol m−2 d−1 (mean SD), whilst at the bare muddy station, EC fluxes ranged from -43.1 mmol m−2 d−1 to 12.1 mmol m−2 d−1 and averaged -15.9 ± 14.0 mmol m−2 d−1 (mean SD) during the total deployment. Eddy Covariance and Benthic Chambers measurements showed similar patterns of temporal flux changes at both sites. However, at the Maerl station, BC may have underestimated community respiration. This may be due to the relative large size of the EC footprint (compared to BC), which takes into account the mesoscale spatial heterogeneity (e.g. may have included contributions from bare sediment patches). Also, we hypothesize that the influence of bioturbation induced by large-sized mobile benthic fauna on sediment oxygen consumption was not fully captured by BC compared to EC. Overall, the results of the present study highlight the importance of taking into account specific methodology limitations with respect to sediment spatial macro-heterogeneity and short-term variations of environmental parameters to accurately assess benthic exchange in the various benthic ecosystems of the coastal zone.