The effects of two small dams of similar size located in different (second order) streams on the Rivers Poio and Balsemao, were studied during one year to assess the impact on the benthic community. In the first stream, regulation is for hydro-power generation purposes and, in the second one, the dam is used to divert water to a small town. These distinct purposes affect the natural hydrological regime differently and the objective was to detect precisely how this reflects on the structure of the benthic communities. Composition of the benthic fauna was compared using multivariate techniques, both below and above the reservoir as well as in this habitat. Variation of diversity along the same reaches was also used to compare the impact on the biota. The results showed that the composition of the invertebrate fauna was only clearly modified downstream of the impoundment on the Balsemao. Here, the longer retention of the water in the artificial lake led to a greater accumulation of allochthonous organic matter, with consequences on the availability of this material below the reservoir, thus modifying the trophic structure. Decrease of diversity was, however, more pronounced in the Poio, reflecting the stress caused by the relatively frequent fluctuations in water flow.