An inventory of the ichthyofauna of the Aquidauana and Miranda basins is presented. A total of 9,559 individuals of six orders, 21 families and 68 species were sampled in streams (n = 6), rivers (n = 2), and reservoirs (n = 5) during the dry and wet seasons. Streams and rivers were the sites with higher richness, with 97% of the total richness. On the other hand, the highest abundance was recorded for reservoirs, with homogeneous assemblages dominated by nektonic species. Structural heterogeneity and proximity to the mainstem seem to be the main factors influencing fish richness in streams. This study reports a high regional richness and reinforces the necessity for the preservation of the lotic environments of the Cerrado.