Biological diversity can be divided into: alpha (α, local), beta (β, difference in assemblage composition among locals), and gamma (γ, total diversity). We assessed the partitioning of taxonomic diversity of Ephemeroptera, Plecoptera and Trichoptera (EPT) and of functional feeding groups (FFG) in neotropical savanna (southeastern Brazilian cerrado) streams. To do so, we considered three diversity components: stream site (α), among stream sites (β1), and among hydrologic units (β2). We also evaluated the association of EPT genera composition with heterogeneity in land use, instream physical habitat structure, and instream water quality variables. The percentage of EPT taxonomic α diversity (20.7%) was smaller than the β1 and β2 diversity percentages (53.1% and 26.2%, respectively). The percentage of EPT FFG collector-gatherer α diversity (26.5%) was smaller than that of β1 diversity (55.8%) and higher than the β2 (17.7%) diversity. The collector-gatherer FFG was predominant and had the greatest β diversity percentage among stream sites (β1, 55.8%). Our findings support the need for implementing regional scale conservation strategies in the cerrado biome, which has been degraded by anthropogenic activities.