Intensive fisheries have reduced fish biodiversity and abundance in aquatic ecosystems worldwide. Networks of no-take reserves have become essential for protecting marine fisheries, but have not been tested in freshwaters. We show that a diffuse set of 23 community-created reserves in Thailand’s Salween basin has increased average local fish richness by 27%, density by 124%, and biomass by 23-fold. Key correlates of reserve efficacy in marine ecosystems—particularly reserve size and enforcement—predict differences in benefits among riverine reserves. Moreover, occupying a central position in the network conferred additional gains, underscoring the importance of connectivity within dendritic river systems. The emergence of network-based benefits is remarkable given that each reserve was designated less than 25 years ago without planning or coordination. In addition, protection from harvest profoundly reconfigured fish assemblages—increasing richness, biomass, and body size—yet mean trophic position remained unaffected. Outside of reserves, harvest intensified trophic interactions through strong non-consumptive effects of surviving fish on grazing insect behavior, extending a three-level trophic cascade observed in reserves to six-levels by linking interactions from humans to algal response to nutrient enrichment. Our findings suggest that networks of small reserves offer an effective and generalizable model for protecting biodiversity and augmenting fisheries as the world’s rivers face unprecedented pressures. Finally, by building on theory that has guided conservation reserve design for the past several decades, we have begun to develop a set of guiding principles for the design of riverine reserve networks in the hopes of accelerating the realization of similar conservation benefits for the world’s rivers.