Shallow-water temperature is an essential factor in various ecosystems, particularly in paddy fields, as damage to paddy rice due to high temperatures may severely affect grain yields. Here, a calculation scheme of paddy field water temperature is proposed to calculate water temperature dynamics in paddy fields and comprises three components: (1) the two-layer heat balance model, which is adopted to calculate water temperature, whereby the solution to the heat balance of paddy water considers the effect of the vegetation layer; (2) a novel method of estimating the plant growth status parameter calculated from thermal storage variations of paddy water to quantify the effect of vegetation layers on water temperature; and (3) a series of correction methods for meteorological parameters to ensure that the parameters measured far from the paddy field are suitable for the model. Estimation of the plant growth status parameter obtained from model validation showed that the proposed method has generality under different weather conditions but with the same rice cultivars. Water temperature calculations showed high consistency, yielding root mean square error values between the measured and calculated water temperatures of 1.65 and 0.91 °C in the full observation period and during the nighttime heatwave period, respectively. Hence, the proposed calculation scheme simplifies the simulating conditions using only the common meteorological factors from the existing weather stations and fundamental paddy factors and simulation of the thermal conditions of paddy fields. This effectively reduces the cost of water temperature calculations.