In the Neotropics, especially in southeastern Brazil, due to sugarcane and eucalypt monocultures, and the expansion of industries and the largely unplanned urban centers entire aquatic ecosystems are threatened. Nonetheless, benthic macroinvertebrates are important biomonitoring tools to assess the biotic and abiotic condition of endangered freshwater environments. In this study we address how benthic macroinvertebrate diversity respond to the combined effect of local environmental factors. We also aimed to evaluate how benthic macroinvertebrates diversity respond according to the habitat integrity. We expected to find higher diversity in the sampling sites with higher habitat integrity (i.e., low potential of hydrogen, electrical conductivity and water temperature, and high canopy coverage and concentration of dissolved oxygen). By using a multivariate approach (i.e., PCA) and a regression analysis (i.e., Linear Mixed-Effect Model) we were able to address the combined effect of local environmental variables on the benthic macroinvertebrate community. Our results show a negative effect of the environmental factors on the benthic macroinvertebrate diversity. As expected, sites with higher integrity and water quality values according to, respectively, the Habitat Integrity Index (i.e., HII) and the Biological Monitoring Working Party (i.e., BMWP’) tended to have higher benthic macroinvertebrates diversity. This is the first report that provides knowledge of the benthic macroinvertebrate community in the Paulicéia river, within the Cerrado Pé-de-Gigante, a conservation unity of full protection of a State Park in the Neotropics.