Freshwater fish are among the most vulnerable taxa to climate change globally but are generally understudied in tropical island ecosystems. Climate change is predicted to alter the intensity, frequency, and variability of extreme flow events on the Caribbean island of Puerto Rico. These changes may impact Caribbean native and non-native stream ecosystems and biota complex ways. We compiled an extensive dataset of native and non-native fish assemblages collected at 119 sites across Puerto Rico from 2005 to 2015. We coupled these data with stream flow indices and dam height to understand how flow dynamics drive fish assemblage structure. Sixteen percent of sites contained exclusively non-native species, 34% contained exclusively native species, and 50% contained a mix of native and non-native species. We built generalized linear models to identify the most critical flow variables for explaining variation in native and non-native species richness and biomass. Mean daily flow was the most important flow variable in driving native species richness (β=-0.06; p<0.05), while flashiness was the most important for non-native species richness (β=1.47; p<0.05). Extreme flow durations were important in explaining variations in native and non-native biomass. Native and non-native biomass decreased by -12.13 kg/ha and -5.93 kg/ha, respectively, with longer annual average low flow durations (p<0.05). Non-native biomass increased by 2.16 kg/ha with longer maximum low flow durations (p<0.05). Annual average low flow durations had a negative effect on both native and non-native assemblages, but the effect on native biomass was twice as large. Native species may be more resilient to one-off extreme low flow events, and non-native species may be more tolerant to the natural flashy flows in the Caribbean than expected. Our results are informative for island ecosystems globally and can guide management and conservation of native fish, particularly in the context of non-native species and climate change. Managers may prioritize maintaining connectivity, refugia and habitat complexity in rivers while preventing non-native fish introductions and establishment to conserve native fish diversity and biomass in Caribbean rivers.