Abstract Hurricanes are major disturbances with important consequences to stream ecosystems as they create major floods and remove riparian vegetation. Understanding their impacts is a priority, as hurricane intensity is expected to increase due to global climate change. Mayfly assemblages in streams fill a diversity of ecological roles and functions. They are important consumers of algae by scraping benthic biofilms and detritivores associated with fine particles and leaf litter. Other taxa are filterers and even predators. Mayflies are also important prey items in aquatic and terrestrial food webs. Here, we assessed the effects of two consecutive hurricanes that impacted Puerto Rico in 2017 to understand how hurricane‐induced changes in the environment alter mayfly composition, secondary production and emergence. The study was conducted in the Luquillo Experimental Forest, Puerto Rico. Mayflies were sampled as nymphs and emerging adults for 6 months before and 17 months after hurricanes Irma and María hit the island in September 2017. Leaf litter inputs, canopy cover and chlorophyll a concentrations were monitored along with mayflies. Mayfly assemblages were dominated by two genera of Leptophlebiidae before the hurricane, Neohagenulus (two species: N. julio Traver, 1938, N. luteolus Traver, 1938) and Borinquena (one species: B. carmencita Traver, 1938). Both genera decreased in density after the hurricanes and were replaced with the Baetidae Cloeodes maculipes Traver, 1938 as the dominant taxon. This pattern was observed in both nymph and emerging adult densities. The secondary production of Leptophlebiidae species was highest before hurricane disturbance, with the Baetidae C. maculipes showing the opposite pattern. Neohagenulus had an annual production of 445 mg m −2 year −1 , C. maculipes of 153 mg m −2 year −1 and B. carmencita of 68 mg m −2 year −1 . Overall, the mayfly assemblages in our studied stream are vulnerable to hurricane disturbances. Expected increases in hurricane impacts might result in assemblage shifts that could change assemblage composition and alter energy flows within the ecosystem.