Inland waters are widely distributed across Antarctica and many have characteristics found only in polar regions. We summarise the diversity of inland aquatic ecosystems and characteristics that make them vulnerable to direct human intervention and environmental variability and change. Primary sources of surface water are ice and snow, rarely rainfall (except in the Maritime Antarctic), restricting flow to the summer melt. Groundwater and sub-glacial systems have been identified but are largely un-investigated. Seasonal freezing imparts considerable variability to the physical habitat of near surface ecosystems. Some water bodies are already impacted by station usage and continuous field investigations that may leave legacies of disturbance. Climate change will greatly alter inland water ecosystems of the continent. Management of direct human activities is through ASPAs, ASMAs and SCAR Codes of Conduct for ‘Terrestrial Scientific Field Research in Antarctica’ and ‘Exploration and Research of Subglacial Aquatic Environments’, with national programme overlays.