AbstractGroundwater exchanges with most lakes are rarely quantified because there are many technical challenges to quantification. We investigated a lakebed mapping approach to infer the relative areas of groundwater exchange in 12 prairie shallow lakes and five Laurentian mixed forest shallow lakes in Minnesota, USA in 2011. We used a relatively common approach (seepage meters) to provide baseline information on the magnitude and direction of flow at four locations in each lake. To expand from point measurements to the whole‐lake scale, we explored use of specific conductivity as a cheaper and more time efficient proxy for groundwater discharge to lakes. We validated the approach at near shore stations in each lake where seepage meter measurements and specific conductivity surveys overlapped. Specific conductivity surveys provided a similar assessment of groundwater discharge compared to seepage meters for 50% of the lake‐sampling period combinations. The lakebed mapping approach, when validated for a lake with a limited number of seepage meter (or alternative methods) measurements, offers the advantages of being more time and labor efficient over the use of a similar number of seepage meter monitoring locations; seepage meters (or piezometers, for example) are costlier in terms of equipment and labor, even for single‐lake studies. We show the combined approach could provide useful baselines for understanding and mapping groundwater exchange in shallow lakes.