Subglacial Antarctic aquatic environments are important targets for scientific exploration due to the unique ecosystems they support and their sediments containing palaeoenvironmental records. Directly accessing these environments while preventing forward contamination and demonstrating that it has not been introduced is logistically challenging. The Whillans Ice Stream Subglacial Access Research Drilling (WISSARD) project designed, tested and implemented a microbiologically and chemically clean method of hot-water drilling that was subsequently used to access subglacial aquatic environments. We report microbiological and biogeochemical data collected from the drilling system and underlying water columns during sub-ice explorations beneath the McMurdo and Ross ice shelves and Whillans Ice Stream. Our method reduced microbial concentrations in the drill water to values three orders of magnitude lower than those observed in Whillans Subglacial Lake. Furthermore, the water chemistry and composition of microorganisms in the drill water were distinct from those in the subglacial water cavities. The submicron filtration and ultraviolet irradiation of the water provided drilling conditions that satisfied environmental recommendations made for such activities by national and international committees. Our approach to minimizing forward chemical and microbiological contamination serves as a prototype for future efforts to access subglacial aquatic environments beneath glaciers and ice sheets.