Physical and chemical variables were measured in 35 lakes from Wood Buffalo National Park, northern Alberta and the Northwest Territories, Canada. Of these lakes, 22 were sinkholes, situated on limestone and gypsum, five were situated on the Canadian Shield and eight were shallow 'muskeg' lakes located on calcareous shales. All of the lakes were small to moderate in size. For each of the 35 lakes, 37 environmental variables were measured. Principal component analysis (PCA) revealed that underlying geology strongly influenced limnic properties. Shield lakes were characterized by higher concentrations of A1 and Fe, and lower pH values, specific conductivities and concentrations of ions such as, Ca, SO4, Li, Mg and Na, than either the sinkhole or the muskeg lakes. The muskeg lakes were differentiated from the sinkhole lakes by decreased Secchi depth owing to higher concentrations of dissolved organic carbon (DOC) and greater productivity, as evidenced by high concentrations of particulate organic carbon (POC) and chlorophyll a. Nitrogen (NH3 and NO2) was also notably higher at these sites.