Protection of Antarctica's biodiversity and ecosystem values is enshrined in the Protocol on Environmental Protection to the Antarctic Treaty, which provides for the designation of Antarctic Specially Protected Areas (ASPAs) to areas with outstanding values. Concern has been raised that existing ASPAs fail to prioritize areas to maximize the likelihood of ensuring the long-term conservation of Antarctic ecosystems and biodiversity. The absence of systematic and representative protection is particularly acute for inland aquatic ecosystems, which support a disproportionate amount of inland biodiversity. This paper promotes the case for overt inclusion of inland waters as a critical component of a representative protected area framework for Antarctica, thereby addressing their current underrepresentation. We set out a structured approach to enable the selection of representative freshwater systems for inclusion in the ASPA framework that, with modification, could also be applied across other Antarctic habitats. We acknowledge an overall lack of information on the biogeography of inland aquatic diversity and recommend increased use of remote data collection along with classification tools to mitigate this, as well as the need for the consideration of catchment-scale processes. Changes that accompany contemporary and anticipated climate change make the need for the conservation of representative biodiversity increasingly urgent.