Major hydroelectric dams are among the principal emergent agents of habitat loss and fragmentation in lowland tropical forests. Arthropods play an critical role in maintaining the health and stability of Neotropical forest ecosystems. Here, we investigate how orchid bees, ants, social wasps, harvestmen and dung beetles responded to the effects of forest habitat loss, isolation and forest canopy degradation induced by a vast hydroelectric reservoir in Central Brazilian Amazonia. The Balbina Dam was built in 1986, resulting in an archipelagic landscape containing 3,546 primary forest islands of varying sizes and degrees of isolation, surrounded by 3,129-km2 of freshwater and standing dead trees. Using scent, malaise and pitfall traps and active searches, we sampled 34 islands, 14 open-water matrix sites, and three mainland continuous forests. Local orchid bee species richness was affected by forest patch area but particularly by patch isolation and our models indicate that body size was a decisive predictor of occupancy rates, with most isolated sites occupied only by a few large-bodied bees. Isolation was the single best predictor of dung beetle species richness, followed by the interaction between isolation and island area, and these variables were key determinants of the relict species composition. We found that 61.5% of all islands retained only a single super-tramp dung beetle species. Harvestmen species richness was unaffected by any local, patch and landscape variables while composition was affected by forest cover. Social wasp species richness was affected only by island area, whereas species composition was affected by isolation and tree species richness. Ant species richness was also unaffected by any of the patch and landscape variables but composition was affected by area. Retaining large forest habitat patches surrounded by large areas of forest cover would minimize forest disturbance and enhance the long-term persistence of arthropods species in large hydroelectric dams, and these measures should be considered prior to the environmental licensing of new dams.