We measured chlorate (ClO3-) and perchlorate (ClO4-) concentrations in ice covered lakes of the McMurdo Dry Valleys (MDVs) of Antarctica, to evaluate their role in the ecology and geochemical evolution of the lakes. ClO3- and ClO4- are present throughout the MDV Lakes, streams, and other surface water bodies. ClO3- and ClO4- originate in the atmosphere and are transported to the lakes by surface inflow of glacier melt that has been differentially impacted by interaction with soils and aeolian matter. Concentrations of ClO3- and ClO4- in the lakes and between lakes vary based on both total evaporative concentration, as well as biological activity within each lake. All of the lakes except the East lobe of Lake Bonney support biological reduction of ClO3- and ClO4- either in the anoxic bottom waters or sediment. The younger less saline lakes (Miers and Hoare), have surface ClO3- and ClO4- concentrations, and ratios of ClO3-/Cl- and ClO4-/Cl-, similar to source streams, while Lake Fryxell has concentrations similar to input streams but much lower ClO3-/Cl- and ClO4-/Cl- ratios, reflecting the influence of a large Cl- source in bottom sediments. ClO3- and ClO4- in Lake Bonney are the highest of all the lakes reflecting the lake's greater age and higher concentration of Cl-. ClO4- appears to be stable in the East Lobe and its concentration is highly correlated with Cl- concentration suggesting that some ClO4- at depth is a remnant of the initial seawater that formed Lake Bonney. ClO3- and ClO4- concentrations provide a simple and sensitive means to evaluate microbial activity in these lakes due to their relatively low concentrations and lack of biological sources, unlike NO3-, NO2-, and SO4-2.