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Evaporation of water bodies is significantly controlled by the available energy (net radiation Rn minus heat storage G). Compared to deep lakes or lakes in the high‐latitude or high‐altitude regions, the heat storage effects of shallow lakes in subtropical regions are less well studied. In this paper, we tested the heat storage effect on the latent heat fluxes estimation using the Priestley‐Taylor (PT) equation and numerical water temperature simulations in an ephemeral and shallow lake, Poyang Lake, in China. Results showed that the estimation bias was significantly correlated with heat storage changes (r = 0.97). Overlooking the impacts of the heat storage changes will induce an increase in the RMSE (root‐mean‐square error) of the evaporation estimation from 10.1 to 54.4 W m−2. Evaporation was overestimated in June and underestimated in August because the daytime Rn tended to be stored in water in June, whereas the heat storage during daytime tended to be released as nighttime evaporation in August, when the vapor gradient between the saturated surface and the air was generally larger than in other months. Water temperature simulations showed that the diurnal changes in the heat storage in the layer that were less than 2 m deep govern G of the total water column. PT estimation of a shallow lake can be improved if the temperature of the top 2 m of water is known. Also, from the modeling perspective, because G was linearly correlated with Rn (r = 0.77), a simple equation (a*Rn + b) that approximates the available energy can improve the evaporation estimate. Key Points: We study the heat storage effect on the PT estimation in an ephemeral and shallow lake, Poyang LakeThe overlook of heat storage induced the RMSE of evaporation estimation increased over three timesThe conversion of heat storage in the water into nighttime LE was the key for evaporation estimation [ABSTRACT FROM AUTHOR]