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Environmental disturbances affect ecosystem functioning through changes in organisms’ metabolism (direct effect) and biodiversity loss (indirect or biodiversity-mediated effect). It is still a challenge to separate direct and biodiversity-mediated effects of environmental changes on ecosystem functioning due to the difficulties in isolating ‘true’ biodiversity loss effects. Furthermore, it is still unclear whether biodiversity-mediated effects are as important as direct effects. In this study, we performed an experiment in artificial microcosms to disentangle biodiversity-mediated and direct effects of two major environmental disturbances on the functioning of aquatic ecosystems: increases in temperature and salinity. The ecosystem function analyzed was the microalgae predation by the zooplankton community (zooplankton grazing rates). Temperature and salinity increases affected the zooplankton grazing rates due to changes in community composition and abundance, as well as organism performance. The impact of salinity changes on community structure was higher than that of temperature; however, the importance of biodiversity-mediated and direct effects was similar to regulating the ecosystem functioning, albeit they have presented different directions and magnitude across the treatments. At a moderate level of temperature increase, we observed that the biodiversity-mediated effect was more relevant than the direct effect, with negative effects on the overall grazing rates. Our results suggest that disturbances can affect the functioning of aquatic environments through a set of complex biological mechanisms that balance direct and biodiversity-mediated effects. We concluded that the relative importance of biodiversity-mediated effects depends on the type and intensity of the disturbance.