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The impact of land use change on regional climate can be substantial but also is variable in space and time. Past observational and modeling work suggests that in a ‘Mediterranean’ climate such as in California’s Central Valley, the impact of irrigated agriculture can be large in the dry season but negligible in the wet season due to seasonal variation in surface energy partitioning. Here we report further analysis of regional climate model simulations showing that diurnal variation in the impact of irrigated agriculture on climate similarly reflects variation in surface energy partitioning, as well as smaller changes in net radiation. With conversion of natural vegetation to irrigated agriculture, statistically significant decreases of 4–8 K at 2 m occurred at midday June–September, and small decreases of ~1 K occurred in winter months only in relatively dry years. This corresponded to reduced sensible heat flux of 100–350 W m
−2
and increased latent heat fluxes of 200–450 W m
−2
at the same times and in the same months. We also observed decreases of up to 1,500 m in boundary layer height at midday in summer months, and marginally significant reductions in surface zonal wind speed in July and August at 19:00 PST. The large decrease in daytime temperature due to shifts in energy partitioning overwhelmed any temperature increase related to the reduced zonal sea breeze. Such changes in climate and atmospheric dynamics from conversion to (or away from) irrigated agriculture could have important implications for regional air quality in California’s Central Valley.