The present study focus on some aspects of zooplankton structure in the Alcantara River (Sicily, Italy), in relation to environmental factors. Zooplankton samplings were performed in spring in four sites, located from up- to downstream along the river course. Four low-flow velocity station points were chosen along a transversal river section in each site. Samples were taken from all station points in the four sites by two different mesh sizes (55 and 100 μm) rectangular nets. Rotifer abundances were an order of magnitude higher in 55 μm mesh size samples than in 100 μm mesh size ones. The two communities also resulted significantly different (ANOSIM test, ρ=0.212; P=0.1%). Generally, low abundances (from 3470±5133 to 422±474 ind.m−3) were explained by low chlorophyll a concentration and the high-flow regime of this river. Rotifer dominated the zooplankton community. Cladocerans, copepods and nauplii occurred with considerably lower abundances than rotifers. However, the relative contributions of these taxa to total abundances depended on the mesh sizes used. Euchlanis and Adineta genera exhibited the highest abundances in the rotifer assemblage. Conductivity alone or in association with temperature and dissolved oxygen was the most important environmental factor affecting rotifer community distribution. Cephalodella sp., Lepadella sp. and Trichotria pocillum showed a high positive relation to pico-plankton, showing this fraction as a possible rotifer food item. This paper demonstrated a higher efficiency of the finest net to characterize riverine zooplankton community that increases from up to downstream in terms of abundances and diversity.