Understanding how ecosystems store or release carbon is one of ecology's greatest challenges in the 21st century. Organic matter covers a large range of chemical structures and qualities, and it is classically represented by pools of different recalcitrance to degradation. The interaction effects of these pools on carbon cycling are still poorly understood and are most often ignored in global-change models. Soil scientists have shown that inputs of labile organic matter frequently tend to increase, and often double, the mineralization of the more recalcitrant organic matter. The recent revival of interest for this phenomenon, named the priming effect, did not cross the frontiers of the disciplines. In particular, the priming effect phenomenon has been almost totally ignored by the scientific communities studying marine and continental aquatic ecosystems. Here we gather several arguments, experimental results, and field observations that strongly support the hypothesis that the priming effect is a general phenomenon that occurs in various terrestrial, freshwater, and marine ecosystems. For example, the increase in recalcitrant organic matter mineralization rate in the presence of labile organic matter ranged from 10% to 500% in six studies on organic matter degradation in aquatid ecosystems. Consequently, the recalcitrant organic matter mineralization rate may largely depend on labile organic matter availability, influencing the CO2 emissions of both aquatic and terrestrial ecosystems. We suggest that (1) recalcitrant organic matter may largely contribute to the CO2 emissions of aquatic ecosystems through the priming effect, and (2) priming effect intensity may be modified by global changes, interacting with eutrophication processes and atmospheric CO2 increases. Finally, we argue that the priming effect acts substantially in the carbon and nutrient cycles in all ecosystems. We outline exciting avenues for research, which could provide new insights on the responses of ecosystems to anthropogenic perturbations and their feedbacks to climatic changes.