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The present study evaluated the response of the zooplankton communities from two reservoirs in the Brazilian semi-arid region to water volume reduction during a long dry season (similar to 2 years). Our hypotheses were that (i) these reservoirs, even when exposed to periods of drought and water reduction, exhibit a temporal variation in the structure of the zooplankton community; and (ii) the adverse conditions typical of semi-arid regions favor an increase in the biomass of opportunist rotifers, especially microphagous species, which can be used as ecological indicators. The reservoirs located in the Brazilian semi-arid region were monitored between 2012 and 2014. The zooplankton was characterized by a considerable richness (42 species) and high dominance of rotifers, especially microphages. Microcrustaceans, which were represented by four small cladoceran species and copepods (calanoid and cyclopoid), were rare and exhibited low abundance. These semi-arid reservoirs were characterized by significant indicator species: F. saltator (IndVal = 99.4 %), B. angularis (IndVal = 99.1%), F. longiseta (IndVal = 98.2 %) and B. havanaensis (IndVal = 94.6 %). Changes in the environmental parameters, resulting from low water volumes and sparse rain, were associated with changes in the zooplankton community, revealing the unique responses of these semi-arid aquatic ecosystems to environmental changes. The largest reservoir maintained a pattern of rotifer dominance, while the smallest underwent drastic changes in environmental parameters and attributes of the zooplankton community.