The Yellowknife Study Area (YSA), Northwest Territories, Canada, was established in 1961 by H. W. Murdy, U.S. Fish and Wildlife Service, for the study of wetland and waterfowl ecology. The study area is located on the western edge of the Precambrian Shield and edge of the taiga and is recognized for its high wetland densities and waterfowl abundance. The region is underlain by discontinuous, warm permafrost and hence vulnerable to a warming climate. The completion of Highway 3 in early 1960s provided the first access to the region for development, research, and monitoring. The YSA is a 38-sq km area centered on Highway 3, extending 48 km in length. In the 1960s, it encompassed 262 natural ponds and 313 man-made ponds created by highway construction. Extensive parts of the highway were moved and substantially improved in 2005, after the last waterfowl study, and portions of the original 1960s highway surface were removed. Within the first 6 years following highway construction in 1961, Murdy collected extensive data on the YSA’s wetlands and waterfowl. In 1962-1965 he collected detailed information on physical features of wetland basins,water quality, and waterfowl populations for 236 ponds. Murdy died before he was able to analyze or publish the wetland data. The original data and aerial photographs are archived at the U.S. Geological Survey, Northern Prairie Wildlife Research Center. The YSA also has been an important area for monitoring and research of boreal waterfowl populations and ecology since the 1960s. The unpublished wetland data decribed here provide a unique opportunity to investigate long-term changes in wetland chemistry, plant communities, and effects of road building. The three datasets included here describes the physical characteristics and water chemistry of the basins. See also companion wetland plant dataset (Northern Prairie Wildlife Research Center, 2017, Wetland plants of the Yellowknife Study Area, 1961-1962). Other data in archived files but not yet digitally archived include depth to permafrost, plant community and species abundance, weather data, and phenology of plants waterfowl, among other details.