This study assessed the effects of hydrological events on aquatic communities at the mesohabitat scale (pool, run, and riffle) in the high Andean region. Four headwater sites located in the Zhurucay microcatchment (southern Ecuador), with elevations higher than 3,500 m, were selected and monitored considering in each site a 50‐m‐long reach and within each reach five cross sections. In each of these reaches, 19 sampling campaigns were conducted in the period December 2011–October 2013, collecting macroinvertebrates and physical characteristics. A total of 27 hydrological indices were calculated using the daily flow rate as input. Large peak flow, small peak flow, and low flow (LF) events were defined based on discharge thresholds. Multivariate statistics showed that 14 hydrological indices were significantly related to the aquatic community. Further, the study revealed that (a) peak events produced stronger effects on communities than LF events, (b) the observed effects of LF events were weaker than those encountered in other latitudes, and (c) local benthic communities have more resilience than similar communities studied in other latitudes.