Environmental factors play an integral role, either directly or indirectly, in structuring faunal assemblages. Water chemistry, predation, hydroperiod and competition influence tadpole assemblages within waterbodies. We surveyed aquatic predators, habitat refugia, water height and water chemistry variables (pH, salinity and turbidity) at 37 waterbodies over an intensive 22-day field survey to determine which environmental factors influence the relative abundance and occupancy of two habitat specialist anuran tadpole species in naturally acidic, oligotrophic waterbodies within eastern Australian wallum communities. The majority of tadpoles found were of Litoria olongburensis (wallum sedge frog) and Crinia tinnula (wallum froglet) species, both habitat specialists that are associated with wallum waterbodies and listed as Vulnerable under the IUCN Red List. Tadpoles of two other species (Litoria fallax (eastern sedge frog), and Litoria cooloolensis (cooloola sedge frog)) were recorded from two waterbodies. Tadpoles of Litoria gracilenta (graceful treefrog) were recorded from one waterbody. Relative abundance and occupancy of L. olongburensis tadpoles were associated with pH and water depth. Additionally, L. olongburensis tadpole relative abundance was negatively associated with turbidity. Waterbody occupancy by C. tinnula tadpoles was negatively associated with predatory fish and water depth and positively associated with turbidity. Variables associated with relative abundance of C. tinnula tadpoles were inconclusive and further survey work is required to identify these environmental factors. Our results show that the ecology of specialist and non-specialist tadpole species associated with ‘unique’ (e.g. wallum) waterbodies is complex and species specific, with specialist species likely dominating unique habitats.