Class A pan evaporation rate, Ep with sediment cover (S) and submerged aquatic macrophytes (Ps) was analysed in a temperate freshwater shallow lake at Keszthely (Hungary), over three growing seasons between 2014 and 2016. The aim was to identify the importance of this water body’s natural components (S and Ps) on Ep. Measured Ep together with reference E of Shuttleworth (E0) and the FAO-56 equation ET were also derived. Pan coefficient, Ka for filled in pans with S and Ps were computed as the ratio of Ep of the planted pan (Ps/S) and Ep. Ka values determined on-site were tested in the estimation of E for an open water body, namely Keszthely Bay of Lake Balaton. Overall seasonal mean evaporation rate was lower for Ep (3.2 ± 1.05 mm day−1) than the seasonal daily average Ep of S (3.7 ± 1.16 mm day−1) and the Ep of Ps (4.0 ± 1.28 mm day−1). Interannual variation of Ep was controlled by variations in seasonal air temperature, Ta. Data of the wet 2014 season showed a significant suppression of Ep, and this was related to humid and cooler weather conditions causing late emergence and early senescence of the submerged macrophytes (Potamogeton perfoliatus L., Myriophyllum spicatum L. and Najas marina L.) at Keszthely Bay. Overall seasonal mean Ka was greater than 1.0 as determined for the three-season time period in pans with S and Ps (Kas: 1.14 ± 0.04; Kap: 1.20 ± 0.05). Except for a previous study from our group (Anda et al., 2016, J Hydrol 542: 615–626) over a two-season period, no such ratio or coefficients have been published, until now. The dominant component of the energy balance was latent heat flux, which accounted for more than 60% of net radiation in Keszthely Bay, depending on Class A pan filling (S and Ps). Diurnal variation in heat storage of the pan also changed due to the occurrence of sediment cover and macrophytes inside the evaporimeters. The most important daily meteorological variables were used to develop the Ep model and to validate S and Ps. Our results show that linear models, even with more input variables, performed better than tree-based models with respect to mean absolute errors (MAE), root mean square errors (RMSE) and determination coefficient (R2) in predicting daily Ep of S and Ps. The use of pan coefficients Kas and Kap increased seasonal E of Keszthely Bay by 4.2, 14.4 and 17.1% during the 2014–2016 seasons, respectively. Total seasonal increments for Keszthely Bay (surface area is about 39 km2) accounted for 0.97, 4.31 and 3.91 million m3 throughout 2014–2016, respectively. In the warmer seasons, an increasing trend in the growth of Keszthely Bay’s E was detected. These results indicate that Class A pan Ep rates need to be modified to take into account sediment cover and submerged macrophytes to derive open water E. This approximation may lend additional credit to the estimation of E in lakes. Given that appropriate estimation of E can effectively impact the management of an ecologically functional lake’s water, maintaining the proper water level and quality can contribute to the sustainability of lakes in the long run.