Habitat fragmentation is a major cause of biodiversity loss in agricultural landscapes. Studying habitat connectivity in fragmented landscapes is therefore pivotal for better understanding the factors that shape faunal communities in anthropogenic landscapes. Amphibians have limited dispersal abilities, strong site fidelity and often perform seasonal movements to reach relatively distant breeding habitats. This calls for a better knowledge of which landscape features might promote dispersal, especially in crops. We applied graph-theoretic network analyses to a set of 35 waterbodies embedded in 10 rice fields in a savanna–rain forest ecotone, Tocantins, Brazil, to assess the importance of landscape features (forest patches, waterbodies) for anuran functional connectivity within the entire network. We used taxonomic, functional and phylogenetic diversity as proxies of anuran functional connectivity (i.e. dispersal ability intrinsic to the taxa), based on previous associations uncovered between species diversity metrics and landscape connectivity. We found that, assuming individuals belonging to each of the 14 amphibian species recorded are unable to disperse over 800 m, forest and waterbody area and abundance are the most important predictors of waterbody importance for connectivity. Hence, pond network connectivity for amphibians in rice crops depends on (1) abundant and large forest patches in the area surrounding waterbodies, and (2) a network of abundant waterbodies.