Lake Superior, the northern-most of the Laurentian Great Lakes, is the largest (by surface area) freshwater lake on the planet. Due in part to its high water surface to land area ratio, over one-third of the Lake Superior basin water budget is derived from precipitation falling directly on the lake surface. For most of the Great Lakes (including Lake Superior), historical precipitation estimates extend back to the early 1880s, and are based primarily on land-based gauge measurements. While alternatives to gauge-based estimates have been explored, there is no clear history of applying regional climate models (RCMs) to improve historical over-lake precipitation estimates. To address this gap in regional research, and to advance the state-of-the-art in Great Lakes regional hydrological modeling, we compare 21 years of output (1980–2000) from an RCM to conventional gauge-based precipitation estimates for the same time period over the Lake Superior basin. We find that the RCM, unlike the gauge-based method, simulates realistic variations in over-lake atmospheric stability, which propagate into basin-wide precipitation estimates with a relatively low over-lake to over-land precipitation ratio in warm months (roughly 0.7 to 0.8 in June, July, and August) and a relatively high over-lake to over-land precipitation ratio in cold months (roughly 1.3 to 1.4 in December and January), compared to gauge-based estimates. Our findings underscore a need to potentially update historical gauge-based precipitation estimates for large lake systems, including Lake Superior, and that RCMs appear to provide a robust and defensible basis for making those updates.