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• Estimating recharge to arid aquifers with various chemical and physical techniques. • Partitioning rainfall infiltration in aquifer recharge by chloride and isotopes. • Estimating groundwater recharge by return flows from agricultural lands. • Providing applied rainfall and return flow recharge coefficients for arid aquifers. Estimation of groundwater recharge is more essential for managing aquifers, particularly in arid regions with limited access to water resources. Low potentiality of aquifer recharge, deep groundwater levels and impacts from other important sources like irrigation return flow add more complexities to estimating recharge in these areas. In this research, physical and chemical (tracer) techniques including water-table fluctuation (WTF), chloride mass balance (CMB), stable isotopes (2H and 18O) and water-budget equation (WBE) were applied to estimate recharge into the Birjand alluvial aquifer in arid areas of SE Iran with a mean annual precipitation of about 147 mm. Recharge rates, in ascending order, were calculated about 5.0, 9.2, 33.2 and 41.7 mm year−1 using isotopes, CMB, WTF and WBE methods, respectively. Isotopes and chloride tracers assessed the rainfall-related aquifer recharge, while the other methods represented total recharge including rainfall infiltration plus deep percolation of irrigation water (irrigation return flow). Total recharge rate of the Birjand aquifer was estimated in average at 37.5 mm year−1, partitioned between the rainfall recharge (7.0 mm year−1) and irrigation return flow (30.5 mm year−1). The values represent an average rainfall recharge coefficient of about 4.8% of the annual precipitation and return flow coefficient of 15% of the total annual applied water for irrigation. Recharge estimates are recommended as initial guesses for calculating water-balance in order to manage valuable groundwater resources in other arid-land aquifers. The study highlighted priorities of the stable isotope and WTF methods in estimating rainfall and total (rainfall + return flows) recharge of the groundwater in arid regions, respectively. [ABSTRACT FROM AUTHOR]