Coralline algal (maerl) beds are widespread, slow-growing, structurally complex perennial habitats that support high biodiversity, yet are significantly understudied compared to seagrass beds or kelp forests. We present the first eddy covariance (EC) study on a live maerl bed, assessing the community benthic gross primary productivity (GPP), respiration (R), and net ecosystem metabolism (NEM) derived from diel EC time series collected during 5 seasonal measurement campaigns in temperate Loch Sween, Scotland. Measurements were also carried out at an adjacent (similar to 20 m distant) permeable sandy habitat. The O-2 exchange rate was highly dynamic, driven by light availability and the ambient tidally-driven flow velocity. Linear relationships between the EC O-2 fluxes and available light indicate that the benthic phototrophic communities were light limited. Compensation irradiance (E-c) varied seasonally and was typically similar to 1.8-fold lower at the maerl bed compared to the sand. Substantial GPP was evident at both sites; however, the maerl bed and the sand habitat were net heterotrophic during each sampling campaign. Additional inputs of similar to 4 and similar to 7 mol m(-2) yr(-1) of carbon at the maerl bed and sand site, respectively, were required to sustain the benthic O-2 demand. Thus, the 2 benthic habitats efficiently entrap organic carbon and are sinks of organic material in the coastal zone. Parallel deployment of 0.1 m(2) benthic chambers during nighttime revealed O-2 uptake rates that varied by up to similar to 8-fold between replicate chambers (from -0.4 to -3.0 mmol O-2 m(-2) h(-1); n = 4). However, despite extensive O-2 flux variability on meter horizontal scales, mean rates of O-2 uptake as resolved in parallel by chambers and EC were typically within 20% of one another.