Baker Creek drains water from subarctic Canadian Shield terrain comprised of a mix of exposed Precambrian bedrock, lakes, open black spruce forest and peat filled depressions. Research in the catchment has focused on hydrological processes at the hillslope and catchment scales. Streamflow is gauged from several diverse sub-catchments ranging in size from 9 to 155 km2. The period of record (2003–2019) of streamflow from these sub-catchments extends from 12 to 17 years, and these data are the focus of this note. Such data are unique in this remote region. 2003–2019 was a period that included both historic wet and dry conditions. Observations during such a diversity of conditions are helping to improve understanding of how stream networks that drain this landscape expand and contract in response to short and long hydroclimatic cycles. These data from a distinctly cold and dry region of low relief, thin soils, exposed bedrock and permafrost are a valuable contribution to the global diversity of research catchment data.