The analytical solution of distributed water table in an unconfined aquifer between streams has been obtained in classic groundwater hydraulics based on Dupuit’s assumption, and it is frequently used in engineering practice. However, the applicability of this analytical model to groundwater in karst fractures needs a further verification. A 2D profile model of discrete fractures in rockmass between streams with equal water levels was simulated, considering a rainfall infiltration rate of 100−800 mm/a. The random fracture network includes two fracture groups, steeply or slightly inclining with the same statistic average aperture of 0.01 cm. Phreatic surface were identified by checking the interface between saturated and unsaturated fractures. The equivalent hydraulic conductivity of saturated fractures was obtained from seepage simulations and compared to the inversely estimated result from the classical analytical solution. It indicates that the relative error of inverse estimation is smaller than 25%. Further, the change in fractures aperture due to dissolution of Karst rocks was simulated with predictions on the state of fractures and quasi-steady state seepage in a 10 ka period. It finds that the maximum of the fracture aperture reaches 0.07 cm, and the classical model can yield an equivalent hydraulic conductivity from water table distribution with the same order of magnitude as the real hydraulic conductivity. The simulation shows an irregular shape of water table and seepage springs on river sides, where the number of springs reduced gradually following the karstification process. Though the classical analytical model can be used to estimate the equivalent hydraulic conductivity of the fractured aquifer between streams, it is unable to reveal the irregular water table shape and predict the change in seepage in Karst fractures.