Summary Biological interactions can alter predictions that are based on single‐species physiological response. It is known that leaf segments of the seagrass Posidonia oceanica will increase photosynthesis with lowered pH, but it is not clear whether the outcome will be altered when the whole plant and its epiphyte community, with different respiratory and photosynthetic demands, are included. In addition, the effects on the Posidonia epiphyte community have rarely been tested under controlled conditions, at near‐future pH levels. In order to better evaluate the effects of pH levels as projected for the upcoming decades on seagrass meadows, shoots of P. oceanica with their associated epiphytes were exposed in the laboratory to three pH levels (ambient: 8.1, 7.7 and 7.3, on the total scale) for 4 weeks. Net productivity, respiration, net calcification and leaf fluorescence were measured on several occasions. At the end of the study, epiphyte community abundance and composition, calcareous mass and crustose coralline algae growth were determined. Finally, photosynthesis vs. irradiance curves (PE) was produced from segments of secondary leaves cleaned of epiphytes and pigments extracted. Posidonia leaf fluorescence and chlorophyll concentrations did not differ between pH treatments. Net productivity of entire shoots and epiphyte‐free secondary leaves increased significantly at the lowest pH level yet limited or no stimulation in productivity was observed at the intermediate pH treatment. Under both pH treatments, significant decreases in epiphytic cover were observed, mostly due to the reduction of crustose coralline algae. The loss of the dominant epiphyte producer yet similar photosynthetic response for epiphyte‐free secondary leaves and shoots suggests a minimal contribution of epiphytes to shoot productivity under experimental conditions. Synthesis. Observed responses indicate that under future ocean acidification conditions foreseen in the next century an increase in Posidonia productivity is not likely despite the partial loss of epiphytic coralline algae which are competitors for light. A decline in epiphytic cover could, however, reduce the feeding capacity of the meadow for invertebrates. In situ long‐term experiments that consider both acidification and warming scenarios are needed to improve ecosystem‐level predictions.

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Although they only occupy a relatively small portion of the surface of the planet, coastal habitats are some of the most productive and valued ecosystems in the world. Among these habitats, tidal flats are an important component of many harbours and estuaries, but their deterioration due to human activities poses a serious threat to biodiversity and ecosystem function. Benthic communities are usually arranged in patches dominated by key species with overlapping distributions. Understanding the ecological consequences of interactions between these species in transition zones where their habitats overlap is necessary in order to quantify their contribution to overall ecosystem functioning and to scale-up and generalize results. Spatial transition in abundance and the interaction of multiple factors that drive ecosystem function are complex processes that require real-world research. Through a multi-site mensurative experiment, we show that transition areas drive non-linear effects on biogeochemical fluxes that have important implications for quantifying overall functioning. In our study the main drivers of ecosystem function were the abundance of two large but functionally very different species rather than biodiversity per se. Furthermore, we demonstrate that the use of the biogenic features created by specific infaunal species at the sediment–water interface is a better predictor of ecosystem functioning than the density of the species per se, making this approach particularly appealing for large scale, mapping and monitoring studies.