The ecological and evolutionary consequences of extreme events are poorly understood. Here, we tested predictions about species persistence and population genomic change in aquatic insects in 14 Colorado mountain streams across a hydrological disturbance gradient caused by a one in 500-year rainfall event. Taxa persistence ranged from 39 to 77% across sites and declined with increasing disturbance in relation to species’ resistance and resilience traits. For taxa with mobile larvae and terrestrial adult stages present at the time of the flood, average persistence was 84% compared to 25% for immobile taxa that lacked terrestrial adults. For two of six species analysed, genomic diversity (allelic richness) declined after the event. For one species it greatly expanded, suggesting resilience via re-colonisation from upstream populations. Thus, while resistance and resilience traits can explain species persistence to extreme disturbance, population genomic change varies among species, challenging generalisations about evolutionary responses to extreme events at landscape scales.