The habitat use by stream fish can provide an understanding of this important component of species niches, and the changes in the availability of certain structures of instream habitats have a strong influence on the occurrence and abundance of fish species. In this study, we identified the interaction networks between fish and microhabitats in 19 streams of three watersheds from the Brazilian savanna, known as the Cerrado. We also investigated whether the connectance between fish species and microhabitats depends on either the species abundance or availability of microhabitats and verified whether the use of stream microhabitats vary among watersheds. The data for the fish were obtained using standardized fish collections and underwater (snorkeling) observations to record the association of fish species with 11 stream microhabitats. We used the incidence data to calculate the connectance of species with different microhabitats, a Spearman correlation analysis to test the dependence of the connectance to the species abundance and microhabitat availability, and an Analysis of Similarity to test whether the use of stream microhabitats by fish can vary among watersheds. In all of the watersheds, the tetras of the family Characidae used the largest number of microhabitats. The most-used microhabitats by the fish watersheds were the lateral surface, column surface, and unconsolidated substrate, which were differentially used by the fish in each watershed, indicating the variable importance of microhabitats. Despite this observation, the fish occurred more frequently in the lateral microhabitats. When the data for all of the streams were combined, the species connectance was correlated with the species abundance. We also discuss the consequences of the elimination of certain bottom structures in the context of siltation, which is the main issue in the studied region. The results of our study allowed the detection of key microhabitat structures and can be used for the aquatic ecosystems restoration. ((c) 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)