Abstract Understanding whether assemblages of species respond more strongly to bottom‐up (availability of trophic resources or habitats) or top‐down (predation pressure) processes is important for effective management of resources and ecosystems. We determined the relative influence of environmental factors and predation by humans in shaping the density, biomass, and species richness of 4 medium‐bodied (10–40 cm total length [TL]) coral reef fish groups targeted by fishers (mesopredators, planktivores, grazer and detritivores, and scrapers) and the density of 2 groups not targeted by fishers (invertivores, small fish ≤10 cm TL) in the central Philippines. Boosted regression trees were used to model the response of each fish group to 21 predictor variables: 13 habitat variables, 5 island variables, and 3 fishing variables (no‐take marine reserve [NTMR] presence or absence, NTMR size, and NTMR age). Targeted and nontargeted fish groups responded most strongly to habitat variables, then island variables. Fishing (NTMR) variables generally had less influence on fish groups. Of the habitat variables, live hard coral cover, structural complexity or habitat complexity index, and depth had the greatest effects on density, biomass, and species richness of targeted fish groups and on the density of nontargeted fishes. Of the island variables, proximity to the nearest river and island elevation had the most influence on fish groups. The NTMRs affected only fishes targeted by fishers; NTMR size positively correlated with density, biomass, and species richness of targeted fishes, particularly mesopredatory, and grazing and detritivorous fishes. Importantly, NTMRs as small as 15 ha positively affected medium‐bodied fishes. This finding provides reassurance for regions that have invested in small‐scale community‐managed NTMRs. However, management strategies that integrate sound coastal land‐use practices to conserve adjacent reef fish habitat, strategic NTMR placement, and establishment of larger NTMRs will be crucial for maintaining biodiversity and fisheries.