In this study, we develop a three-dimensional (3-D) numerical model using COMSOL Multiphysics to estimate water evaporation from open-water bodies, rigorously validated against experimental data from the literature, demonstrating satisfactory accuracy. Through comprehensive simulations, we elucidate the evolving patterns of evaporation with natural convection in diverse environmental conditions, including temperature, wind speed, and relative humidity. Specifically, under windless conditions, the evaporation rate initially decreases due to moisture accumulation and subsequently increases, as determined by the temperature at the air–water interface. In contrast, under windy conditions, the evaporation rate consistently decreases, solely dictated by this temperature. In addition, our findings underscore the critical role of natural convection within the water body in influencing evaporation rates under both windy and windless conditions. Specifically: 1) Neglecting the contribution of natural convection within the water body results in significant discrepancies in evaporation rate estimations, over 2.5 times in windless conditions, 2.5 times at 2 m/s, and 1.5 times at 5 m/s, due to the lower heat transfer rate of conduction compared to convection. 2) In the absence of external heat input, the omission of natural convection reduces the evaporation rate by 2 times under windless conditions, 1.05 times at 2 m/s, and 1.02 times at 5 m/s. Finally, the roll pattern of Rayleigh–Bénard convection in a water body is analyzed, which is primarily dominant by external heat, even in windy conditions. Without external heat, the wind takes over as the main factor affecting the evaporation rate. In the absence of both external heat and wind, natural convection in the air becomes the dominant factor for evaporation. This numerical investigation expands the validity of current methods for estimating evaporation from open-water bodies under complex environmental conditions.