Groundwater resources have been extensively explored in Wadi Al-Fara coastal catchment, located at the northwest of Oman, to supply agricultural, industrial and domestic demands. Consequently, groundwater level has declined, which calls for urgent mitigation strategies to sustain the groundwater resources. Reasonable knowledge of natural recharge to a groundwater basin is fundamental for its sustainability and management. Thus, recharge was estimated using different methods including chloride mass balance (CMB), water table fluctuation (WTF) and groundwater modeling methods in Wadi Al-Fara catchment. Based on the CMB method, the recharge is respectively estimated at about 45 and 8 mm/year for the highland and coastal zones. According to the WTF method, the recharge is estimated as 10–22 mm/year and 6–14 mm/year in the plain and coastal zones, respectively. Modeling showed that a long-term regional groundwater recharge is about 31 Mm3 /year (26 mm/year) for the whole study area, and the long-term lateral flux from the highland to the coastal zone (12 Mm3 /year) is a major contributor to water resources in the coastal plain.