The surface of the Great Lakes interacts with the atmosphere, influencing the weather and climate over the Great Lakes Region (GLR). However, most climate models were not designed with sufficient emphasis on lake–atmosphere interactions, which could potentially cause model biases over the GLR. To understand how lake surface temperature (LST) affects the regional summer climate over the GLR, we conducted twin experiments using the Weather Research and Forecasting model at a spatial resolution of 4 km using two different LST data sets as the bottom boundary condition over the Great Lakes. Our simulations include 10 ensemble members for the summer of 2018 and a single multiyear run for the summers of 2014–2020. Results show that variations in LST influence atmospheric temperature and moisture at a local scale—while affecting the convective environment and precipitation processes over a much larger spatial scale. In particular, an LST that is only 1°C–3°C warmer (depending on the lake) increases near‐surface air temperature by 1.93°C and 0.97°C over Lake Superior and Lake Erie, respectively, and increases evaporation over the lakes by 0.23 and 1.1 mm day−1. The warmer LST reduces mesoscale convective precipitation upstream of the GLR; however, it increases isolated deep convective precipitation and nonconvective precipitation downstream of GLR due to increased local instability and enhancement of moisture transport. Our analyses confirm the robustness of these impacts, which is at least 2 times larger than the model internal variability and is seen across all simulated summer seasons.