Species-environment relationships are important to assess the biological patterns, mainly those related to spatial distribution, since species undergo seletive pressure along their evolutive history, which determine the success in colonizing habitats. In fluvial ecosystems the geomorphology can acts as a constraint for fish species distribution, by determining kinds and levels of habitats structuring to which species are associated. This work aims to address the relationship between fluvial geomorphology and fish assemblages from Paraiba do Sul watershed, in an attempt to explaining the underlying spatial assemblages distribution patterns. Additionally, we assess the use of two river classification systems, developed for temperate regions, to this case study. Thirty-seven sites along the watershed were sampled during the dry season (May-October) between 2003 and 2005. The rivers were classified in three size categories: small (1a. to 3a. Order), medium (4a. to 6a. order) , and larger (> 6a. order), based in fluvial hierarchical classification scale. Fishes and geomorphological variables were sampled in a stretch of approximately 20 times the width for small and medium rivers, and in approximately 1 km for large rivers. Four fish assemblages were detected by cluster analysis and non-metric multidimensional scales – MDS; one dominated by Tricomycterus immaculatum and Neoplecostomus microps, corresponding to small and medium rivers from hillslopes, straigths, with high slopes and channel showing bedrock, step-pool, and cascade. The second, dominated by Rhamdia quelen, Astyanax parahybae and Harttia loricariformis and the third, by Phalloceros caudimaculatus and Geophagus brasiliensis, corresponding to meandering rivers, with low and moderated slopes, channels showing pool-riffles, non-entrenchment, with channels associated to floodpains areas. The fourth assemblages is dominated by A. bimaculatus and Oligosarcus hepsetus, which are widely distributed along all watershed; in the lower reaches Loricariichthys spixii occurs in high frequency as well as eurihalines marine species, corresponding to low and medium sinuosity rivers with low slopes, channels showing pool-riffle, dune-ripple and braided, large cross-section, flooplains well developed and bed formed by gravel and sand. Slope, entrenchetment and width-depth ratio were the main constraints controlling the habitat. Our results match the main predictions of the Process Domain Concept (PDC) which postulate that fish assemblages vary in response to local habitat characteristics and the richness is directly associtated to cross-section area, contrasting with the prediction of the River Continuum Concept which postulate that assemblages vary previsible along the longitudinal gradient.