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Quantification of groundwater recharge is of fundamental importance for groundwater modeling, planning, management, and sustainable utilization of limited water resources, especially in arid and semi-arid environments such as the eastern part of Iran. Numerous techniques are used to quantify recharge rate based on certain hydro-geological conditions. In this study, based on available hydro-geological information, cumulative rainfall departure (CRD) and rainfall infiltration breakthrough (RIB) methods were selected to estimate the groundwater recharge. These methods are based on the water balance principle (rainfall-groundwater level relationship) and require few non-deterministic data such as groundwater level measurements, rainfall, aquifer properties, and groundwater extraction dataset. These methods were modified to provide the percentage of return flow and rainfall contributions to natural groundwater recharge. The study area was split to polygons based on the existing observation wells. The natural recharge rate was estimated for each Thiessen polygon on a monthly basis. Utilizing of these two methods, groundwater levels were simulated, and the optimization technique was also applied to minimize the root mean square error between the simulated and observed groundwater levels. The results were shown that the simulated groundwater levels were matched well with the observed values. The recharge areas were then mapped using these two methods. As an average 13 and 27 % of cumulative rainfall departure and return flow contributed to groundwater recharge for whole study area by applying CRD model, whereas by RIB these values were 11 and 19 %, respectively. The average annual recharge rate estimated for Neishaboor Plain, using RIB and CRD were 160 and 164 mm, respectively.