Equatorial glacier-fed streams present unique hydraulic patterns when compared to glacier-fed observed in temperate regions as the main variability in discharge occurs on a daily basis. To assess how benthic fauna respond to these specific hydraulic conditions, we investigated the relationships between flow regime, hydraulic conditions (boundary Reynolds number, Re*), and macroinvertebrate communities (taxon richness and abundance) in a tropical glacier-fed stream located in the high Ecuadorian Andes (> 4000 m). Both physical and biotic variables were measured under four discharge conditions (base-flow and glacial flood pulses of various intensities), at 30 random points, in two sites whose hydraulic conditions were representative to those found in other streams of the study catchment. While daily glacial flood pulses significantly increased hydraulic stress in the benthic habitats (appearance of Re* > 2000), low stress areas still persisted even during extreme flood events (Re* < 500). In contrast to previous research in temperate glacier-fed streams, taxon richness and abundance were not significantly affected by changes in hydraulic conditions induced by daily glacial flood pulses. However, we found that a few rare taxa, in particular rare ones, preferentially occurred in highly stressed hydraulic habitats. Monte-Carlo simulations of benthic communities under glacial flood reduction scenarios predicted that taxon richness would be significantly reduced by the loss of high hydraulic stress habitats following glacier shrinking. This pioneer study on the relationship between hydraulic conditions and benthic diversity in an equatorial glacial stream evidenced unknown effects of climate change on singular yet endangered aquatic systems.