We examined the effects of longitudinal discontinuity in small rivers, produced by the construction of small dams, on the macroinvertebrate communities in a biological reserve in southeastern Brazil. Two regulated streams were sampled in the rainy and dry seasons at three sites along the river. One site was upstream of the dam/abstraction and two were below the dam. Our results indicate that there was a difference in the communities between the dry and rainy periods even though water physicochemical parameters of the water were not significantly different. The biotic richness at sites 500 m below the dam were similar to those above the impoundment (control), indicating that the fauna recovered when the discharge values found before water abstraction were reestablished. We concluded that the dam did induce changes in the composition of benthic comunities, especially in the dry period. However, overall, the fauna seemed to be able to persist during periods when the flow was absent.