Estimating base flow rate and ground water recharge in a watershed is one of the most important issues in the  management of water resources and hydrology. Since the river-aquifer system is a system with two inter-related elements, it is necessary to investigate base flow versus groundwater table of the aquifer to evaluate groundwater recharge estimation methods. In this study, PART and RORA software packages were used for base flow separation and groundwater recharge estimation based on the daily flow data for the Chenar Rahdar River. Also, the correlation between estimates of the two methods and groundwater levels was calculated. In this study, RORA was used to estimate the mean annual recharge during the statistical period using a recession curve displacement method which gave an estimate of 329 mm; using PART a discharge rate of 301 mm was estimated. RORA estimates the recharge rate above the discharge rate. The results of this study showed that there is an inverse relationship between estimates of the two methods with groundwater table. The average base flow index represents 65 percent of the overall flow at the station. Also statistical tests showed no significant differences between rates of groundwater discharge and recharge.