The aim of this study was the assessment of the utilization of two methods, i.e. the Thornthwaite and the Turc equations, for the analysis of the water balance in an environmentally sensitive area. The hydrologic balance of a basin consisting in two lakes (Zazari and Cheimaditida) in northern Greece, and covering an area of 228 km² has been estimated. The Thornthwaite method was applied in the study area, for the calculation of the evapotranspiration factor and was compared to the results obtained by the application of the Turc method in the same area. For the development of these equations and the calculation of the evapotranspiration rates, monthly temperature and precipitation values collected from meteorological stations over a period of 30 years were used. The utilization of monthly average temperatures in the Thornthwaite equation resulted to an actual evapotranspiration rate of ΕT = 412.7 mm (80.23%) for p = 514.4 mm and a runoff rate of Q = 101.7 mm (19.77%). However, the Turc equation gave slightly higher values i.e. ET = 428.8 mm. Nevertheless, the application of the Turc equation, using the corrected temperature factor T _c, resulted to the calculation of an evapotranspiration value similar to the corresponding estimated by the Thornthwaite equation, indicating that the utilization of the former method could be favored, due to its simplicity over the latter one.