Tropical freshwater ecosystems represent one of the planet’s most biodiverse ecosystems, but also one of the most endangered in the world compared to marine and terrestrial ecosystems. Freshwater ecosystems are exposed to multiple local- and global-scale stressors but little is known of their synergistic effects. It has proven challenging to study the impacts of multiple environmental stressors on ecosystem functioning through their effects on biological diversity, first because effects on single species cannot be extrapolated to the complex network of species interactions, second because most of our current understanding of biodiversity-ecosystem function relationships has come from investigations of the response of ecosystem function in isolation neglecting the simultaneous responses of multiple functions (i.e., “multifunctionality”). The aim of INTERACTIF is to tease out the pure and interactive effects of local- and global-scale environmental stressors on different levels of biological organisation ―communities, ecological networks, ecosystems― in neotropical freshwater ecosystems. We will use freshwater microcosms formed by rainwater-filled leaves of tank bromeliads and their microbial-faunal communities to test ecological hypotheses related to the effects of multiple stressors on biological communities to ecosystem functions in manipulative experiments. Cross-habitat transplantations and rainout shelters will be used to examine how the effects of emulated changes in forest canopy cover (deforestation) and precipitation (drought), and their interaction, propagate from communities to ecosystems. DNA-based metabarcoding will allow us to characterise the overall aquatic community and to examine the effects of multiple stressors on high-resolution ecological networks. Based on current theory, we expect that a shift from closed to open forest canopy with deforestation will lead to a shift from brown (detritus-based) to green (algae-based) food webs, as allochtonous subsidies (leaf litter inputs) will decline and incident light will increase. Drought in isolation is expected to induce a similar shift towards green food webs by concentrating nutrients as water volumes decline during the drought spell. A combination of these types of disturbance should therefore exacerbate the trend towards green food webs. However, the subsequent direction and magnitude of changes in ecosystem multifunctionality are unknown and remain to be investigated. Importantly, we take advantage of ecological network analyses to bring out causal relationships between changes in environmental conditions, ecological network topology, and the production of key ecosystem functions such as leaf litter decomposition, microbial respiration, and algal photosynthesis. INTERACTIF comes at a critical point in research on the ecological effects of multiple environmental changes in neotropical freshwater ecosystems. In this context, it will aim at understanding the mechanisms that enhance or undermine species diversity, biological interactions, and ecosystem functions, and ultimately help predicting the fate of freshwater ecosystems in response to habitat alteration and drought.