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Abstract Lake surface conditions are critical for representing lake‐atmosphere interactions in numerical weather prediction. The Community Land Model's 1‐D lake component (CLM‐lake) is part of NOAA's High‐Resolution Rapid Refresh (HRRR) 3‐km weather/earth‐system model, which assumes that virtually all the two thousand lakes represented in CONUS have distinct (for each lake) but spatially uniform depth. To test the sensitivity of CLM‐lake to bathymetry, we ran CLM‐lake as a stand‐alone model for all of 2019 with two bathymetry data sets for 23 selected lakes: the first had default (uniform within each lake) bathymetry while the second used a new, spatially varying bathymetry. We validated simulated lake surface temperature (LST) with both remote and in situ observations to evaluate the skill of both runs and also intercompared modeled ice cover and evaporation. Though model skill varied considerably from lake to lake, using the new bathymetry resulted in marginal improvement over the default. The more important finding is the influence bathymetry has on modeled LST (i.e., differences between model simulations) where lake‐wide LST deviated as much as 10°C between simulations and individual grid cells experienced even greater departures. This demonstrates the sensitivity of surface conditions in atmospheric models to lake bathymetry. The new bathymetry also improved lake depths over the (often too deep) previous value assumed for unknown‐depth lakes. These results have significant implications for numerical weather prediction, especially in regions near large lakes where lake surface conditions often influence the state of the atmosphere via thermal regulation and lake effect precipitation.