AbstractSpecies extinctions have the potential to dramatically reshape ecological communities. In the Sierra Nevada mountains of California, the emergence of a lethal amphibian pathogen (Batrachochytrium dendrobatidis) drives mountain yellow‐legged frog (Rana muscosa and Rana sierrae) populations to local extinction. Prior to population declines, these frogs and their tadpoles were abundant, high‐level predators and grazers with high trophic connectance. To quantify how these low diversity aquatic macroinvertebrate communities respond to nonrandom single‐species local extinctions, we quantified aquatic macroinvertebrate communities using two approaches: a natural experiment (“Resurveys”) and a large‐scale synoptic observational study (“Snapshot” surveys). In the Resurveys, we compared benthic macroinvertebrate communities in 22 Sierra Nevada alpine lakes that we categorized as either having extant frog populations, experiencing ongoing disease‐driven frog declines, or having previously experienced local disease‐driven frog extirpation. In the Resurveys, taxonomic richness was about one taxa (17%) higher in lakes where frogs were declining or extinct, compared to lakes where frogs were extant. However, multivariate analyses revealed no strong dissimilarities among Resurvey communities, and there were no differences in the abundances of individual taxa between lakes in the frogs extant, declining, or extinct categories. In the Snapshot surveys, we reanalyzed previously collected data from a large‐scale survey of 157 lakes with and without frogs. In the Snapshot survey, invertebrate taxonomic richness was less than one taxa (9%) lower in lakes without frogs, and multivariate analyses again indicated only small differences between lakes with and without frogs. Overall, disease‐driven mountain yellow‐legged frog extinctions had small effects on lake benthic macroinvertebrate communities, with no large changes in invertebrate abundance, richness or evenness, no clear secondary extinctions or invasions, and few taxa showing distinct responses to frog extinctions. Our study highlights how even for conspicuous, highly connected, omnivorous taxa that are experiencing large, rapid, and widespread declines and extinctions, the ecological effects of extinctions will sometimes be small and subtle.