These data include base flow separation estimates for 64 USGS streamflow gages in the Lake Superior watershed from 1945 to 2020, shapefiles of the gaging stations and watersheds for each gaging station, and a zipped folder of graphics of the base flow separation results. The base flow separation estimates were calculated using the U.S. Geological Survey Groundwater Toolbox (Barlow and others, 2014) for any complete water years of record for these gages from 1945 to 2020. The shapefile of the gaging stations includes the starting and ending years of data for each station, the number of years of record. The watersheds shapefile includes the source for the watershed delineation, the watershed area, and the number of upstream and(or) downstream gaging stations on the same river system. If there are upstream gaging stations in the river system, the watershed delineated is only the incremental part of the watershed between gaging stations. The baseflow separation estimates for each gaging station include daily, monthly, and annual output from the Groundwater Toolbox for six estimation methods included in the software (full references are available in Barlow and others, 2014): the baseflow Index-Standard method, HySep Fixed Interval, HySep Local Minimum, HySep Sliding Interval, baseflow Index-Modified, PART, and BFLOW. A summary of the annual baseflow estimates for all the gaging stations using all the methods is provided also is included in this data release. This data release is one of three child items under the overall data release at https://doi.org/10.5066/P9084UKQ.