Water availability significantly influences bird and mammal ecology in terrestrial ecosystems. However, our understanding of the role of water as a limiting resource for birds and mammals remains partial because most of the studies have focused on surface water bodies of desert and semi-desert ecosystems. This study assessed the use of two types of surface water bodies (waterholes and epikarst rock pools) and one arboreal (water-filled tree holes) by birds and mammals in the seasonally dry tropical forests of the Calakmul Biosphere Reserve in southern Mexico. We deployed camera traps in 23 waterholes, 22 rock pools, and 19 water-filled tree holes in this karstic region to record visits by small, medium, and large-bodied birds and mammals during the dry and rainy seasons. These cameras were set up to record videos documenting when animals were making use of water for drinking, bathing, or both. We compared the species diversity and composition of bird and mammal assemblages using the different types of water bodies by calculating Hill numbers and conducting non-metric multidimensional scaling (NMDS), indicator species, and contingency table analyses. There was a greater species richness of birds and mammals using surface water bodies than tree holes during both seasons. There were significant differences in species composition among bird assemblages using the different water bodies, but dominant species and diversity remained the same. Terrestrial and larger mammalian species preferentially used surface water bodies whereas arboreal and scansorial small and medium mammals were more common in arboreal water bodies. These findings suggest that differences in water body characteristics might favor segregation in mammal activity. The different water bodies may act as alternative water sources for birds and complementary sources for mammals, potentially favoring species coexistence and increasing community resilience to environmental variation (e.g., fluctuation in water availability). Understanding how differences in water bodies favor species coexistence and community resilience is of great relevance from a basic ecological perspective but is also crucial for anticipating the effects that the increased demand for water by humans and climate change can have on wildlife viability.