Abstract Lakes are globally important sources of atmospheric methane (CH4), yet a process‐based understanding of their emissions and drivers at regional scales remains limited. Here we developed and applied a one‐dimensional lake model to 42,948 natural lakes across the contiguous United States (CONUS). Simulations indicate that ebullition is the dominant emission pathway, contributing ∼70% of total fluxes, particularly in shallow, eutrophic systems. Shallow benthic zones act as emission hotspots, accounting for ∼85% of lake CH4 emissions. CONUS lakes oxidize ∼65% of produced CH4 on average, with oxidation efficiencies ranging from 46% in shallow lakes to 92% in deeper systems. Scenario analyses demonstrate that warming and nutrient enrichment jointly drive strong, nonlinear increases in lake CH4 emissions by preferentially enhancing ebullition. Our results indicate that nutrient management offers a practical and effective pathway to mitigate future lake CH4 release and weaken anthropogenic climate feedbacks.