There is a worldwide concern on the loss of pond biodiversity in human dominated landscapes. Nevertheless, agricultural activities appear to increase pond number in the Brazilian Cerrado through damming streams for cattle raising. These man-made ponds may represent important landscape features, but their importance to regional biodiversity has not yet been studied. Here, we evaluated differences in alpha and beta diversity under a multi-taxonomic approach, as well as tested pond size as the main driver of local species richness. We also assessed the importance of environmental heterogeneity through the analysis of the regional species accumulation curves (SAC). The overall result suggests that species turnover was the major component of regional biodiversity for all groups. Major physical and chemical water conditions had no effects on algae, macrophytes, water bugs, and birds species richness. Pond size had a significant effect on Odonata and fish species richness, while water beetles and amphibians were influenced by trophic conditions. Results from regional SAC show variations among different taxonomic groups regarding landscape heterogeneity: only algae, fish, and birds do not reached to an asymptote and had higher z-values. Our results highlight the importance of ponds for biodiversity conservation in increasingly agricultural landscapes in central Brazil.