Water conservation efforts for California’s agricultural industry are critical to its sustainability through severe droughts like the current one and others experienced over the last two decades. This is most critical for perennial crops, such as vineyards and orchards, which are costly to plant and maintain and constitute a significant fraction of the regional water use. It is no longer feasible to access groundwater for irrigation to replace deficit surface water resources during drought due to a significant overdraft of aquifers and new regulation limiting its use. To achieve significant water savings, the actual crop water use or evapotranspiration (ET) needs to be mapped from field to regional scales on a daily basis. This can only be achieved using remote sensing-based models, particularly thermal-based energy balance models that are sensitive to deficit irrigation conditions. The two-source energy balance (TSEB) model has been successfully applied over vineyards in California, but challenges still remain. In particular, much of the irrigated cropland in the California Central Valley is affected by advection of hot dry air masses from surrounding non-irrigated areas and the TSEB model appears to need modifications to adequately estimate ET under such conditions, as well as the partitioning between evaporation and transpiration. This study investigates the application of the TSEB model, using local observations in a vineyard having significant advection. Four versions of the transpiration algorithm in TSEB are applied and evaluated with tower eddy covariance measurements spanning 4 growing seasons. The results suggest the performance of the original transpiration algorithm based on Priestley–Taylor used in TSEB is satisfactory in all but the most extreme advective conditions, while a transpiration algorithm based on Shuttleworth–Wallace with a canopy resistance formula, which relates maximum stomata conductance to vapor pressure deficit (VPD), performs well in all cases. These modifications have potential for improving regional applications of the TSEB model in support of water management in the Central Valley.