Stream ecosystems in Puerto Rico have flashy hydrologies that favor native species, rather than the expected non-native ones. However, a drought allowed Red Devil cichlids to become dominant in the main urban watershed in the San Juan Metropolitan Area. We assessed macroinvertebrate assemblage composition and structure to understand potential changes due to the presence of non-native fish populations. Three sites along the Rio Piedras main stem were selected and two reaches were delimited (control and fish manipulation) in each site. We sampled macroinvertebrates, chlorophyll, and benthic organic matter at each reach before and two months after the removal of non-native fishes in the manipulation reach. Benthic macroinvertebrate assemblages were dominated by Chironomidae (Diptera), followed by three genera of mayflies, one snail, and worms. Overall, 67 taxa were found in the Rio Piedras. Macroinvertebrate abundance reflected changes in hydrology. Our March sampling coincided with a rainy period, while June with a dry spell. Macroinvertebrate abundance was low during March and highest in June. Non-native fish removal had no effects on macroinvertebrate abundance and biomass. However, ordination analysis highlighted differences in assemblage composition and structure between control and fish removal. Differences were related to changes in the dominant groups of Chironomidae in the Upper and Middle reaches, while Americabaetis (Ephemeroptera) became dominant in the Lower reach. Overall, our study highlights the importance of short life cycles as a strategy for macroinvertebrates inhabiting this tropical urban river. Although fish effects were relatively minor, the presence of red devils has a significant impact on the structure of benthic communities.