One of the forest types occurring in Southern Brazil is the Mixed Ombrophilous Forest (MOF), a subtype of the Atlantic Forest and one of the biodiversity hotspots on Earth. We sampled adult Odonata at 30 locations in the Floresta Nacional de São Francisco de Paula (FLONA-SFP), Rio Grande do Sul, Brazil, a national reserve which is divided into several sectors of MOF, planted Araucaria angustifolia, Pinus elliottii used for sustainable and financial purposes, and open fields. There are three types of aquatic environments in the reserve: lakes, swamps, and rivers/streams. Our aim was to obtain an overview of the species’ distribution patterns in the three types of aquatic environments and to evaluate the species occurring in lakes, an exclusively man-made habitat in this area. We recorded 46 species from seven odonate families; 25 species (x = 5.71 ± 1.77 SD) occurring in rivers/ streams, 24 in lakes (11.57 ± 2.15) and 21 in swamps (5.22 ± 3.60). Using Non-metric Multidimensional Scaling (NmDS), we showed that the species composition differed clearly between the three types of aquatic habitats. While swamps and rivers/streams had a relatively similar and uniform species composition, species in the lakes were more varied but the total species number was almost as high as that of the rivers/streams. The lake communities also differed distinctly from those of the other habitats, and we assume that the lake species originate from other degraded areas in the vicinity, indicating that the remains of the Atlantic Forest has already been strongly altered by humans. Given the poor knowledge of the Odonata in the Atlantic Forest/MOF, we hope that our study may increase the understanding of the communities, and contribute to the development of conservation measures for this fragmented biome.