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Predators can have dramatic effects on food web structure and ecosystem processes. However, the total effect of predators will be a combination of prey removal due to consumption and non-consumptive effects (NCEs) mediated through changes to prey behavioral, morphological, or life history traits induced to reduce predation risk. In this study, we examined how consumptive and NCEs alter community composition and ecosystem function using the aquatic ecosystem housed within tropical bromeliads. We allowed the recolonization of emptied bromeliads containing either no predators, caged predators (NCEs only), or uncaged predators (NCEs and consumptive effects) and recorded densities of all macro-invertebrates, microbial densities, and in situ CO2 concentrations after 30 days. We found that predators altered community composition and CO2 concentrations largely through NCEs. The magnitude of the effects of NCEs was substantial, contributing more than 50% of the total effects of predators on macro-invertebrate communities. The NCEs of predators were also strong enough to generate a trophic cascade, which significantly increased micro-organisms and ecosystem respiration, which led to increased in situ CO2 concentrations. The most likely mechanism behind the NCEs on macro-invertebrate density was detection of predator cues by ovipositing adult females, who actively choose to avoid bromeliads containing predators. Through this mechanism, predator NCEs modified community colonization, the structure of food webs, populations of lower trophic levels, and ecosystem processes performed by the community. We therefore propose that quantification of the relative strength of predator NCEs in natural ecosystems is critical for predicting the consequences of predator loss from the world’s ecosystems.