Abstract Food webs depict the tangled web of trophic interactions associated with the functioning of an ecosystem. Understanding the mechanisms providing stability to these food webs is therefore vital for conservation efforts and the management of natural systems. Here, we first characterised a tropical stream meta‐food web and five individual food webs using a Bayesian Hierarchical approach unifying three sources of information (gut content analysis, literature compilation and stable isotope data). With data on population‐level biomass and individually measured body mass, we applied a bioenergetic model and assessed food web stability using a Lotka–Volterra system of equations. We then assessed the resilience of the system to individual species extinctions using simulations and investigated the network patterns associated with systems with higher stability. The model resulted in a stable meta‐food web with 307 links among the 61 components. At the regional scale, 70% of the total energy flow occurred through a set of 10 taxa with large variation in body masses. The remaining 30% of total energy flow relied on 48 different taxa, supporting a significant dependency on a diverse community. The meta‐food web was stable against individual species extinctions, with a higher resilience in food webs harbouring omnivorous fish species able to connect multiple food web compartments via weak, non‐specialised interactions. Moreover, these fish species contributed largely to the spatial variation among individual food webs, suggesting that these species could operate as mobile predators connecting different streams and stabilising variability at the regional scale. Our results outline two key mechanisms of food web stability operating in tropical streams: (i) the diversity of species and body masses buffering against random and size‐dependent disturbances and (ii) high regional diversity and weak omnivorous interactions of predators buffering against local stochastic variation in species composition. These mechanisms rely on high local and regional biodiversity in tropical streams, which is known to be strongly affected by human impacts. Therefore, an urgent challenge is to understand how the ongoing systematic loss of diversity jeopardises the stability of stream food webs in human‐impacted landscapes.