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-square 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, 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 1961-1962 he recorded wetland plant species occurring in each of the 236 ponds and categorized their abundance. 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 The unpublished wetland data described here provide a unique opportunity to investigate long-term changes in wetland plant communities and effects of road building. Related are three datasets describing other aspects of the YSA ponds (see Northern Prairie Wildlife Research Center, 2017, Wetlands of the Yellowknife Study Area, 1963-1965: Characteristics. U.S. Geological Survey data release, https:/dx.doi.org/10.5066/P9YXSNW5). Other data in archived files but not entered or digitally archived include depth to permafrost, selected upland plant communities, weather data, and phenology of plants and waterfowl, among other information.