Abstarct: Gonabad area is an arid and semi-arid region is situated in the south of Razavi Khorasan province. Qanats or Karizs are the most important method for the exploitation of groundwater in this area. In Gonabad Plain, 19.5 million cubic meters of groundwater is annually extracted from 26 branches of qanat whose discharge rates vary from 10 to 120 lit/s. Qanats supplies irrigation and drinking water in the area, therefore it is necessary to determine the catchment area, water budget calculation in catchment area, discharge decrease trend, effect of groundwater drowdown on discharge decrease and recharge origin and mechanism of the qanats. In order to determine these parameters, in this research hydrogeological, hydrogeochemical and isotopic characteristics of the groundwater of qanats were done. The total catchment area of Gonabad Plain Qanats was determined which its surface area is 1032 km2. Water budget calculation in the catchment area shows that 3.7 MCM of groundwater more than catchment recharge and from aquifer storage was extracted annually which led to 0.06 meter per year groundwater level drawdown in catchment aquifer and decrease in qanats water bearing zone. Variations in effective precipitation (dialy precipitation more than 20 mm) of catchment altitudes along changes in discharge of qanats were perused. Annual discharge decrease rate of qanats was calculateded 0.17 to 1.17 liter per second per year. The annual discharge decrease rate of Rahn Qanat is the most. The recharge of this qanat takes place through carbonate formations (Jamal and Shotori Formations). Thus, the groundwater type of this qanat is carbonate leading to the intensive precipitation of carbonate compounds in the qanat’s tunnel. Hence, due to the lack of dredging for several years the discharge of the qanat has dropped sharply. The least annual discharge decrease rate calculated in Dizagh Qanat. High specific yield of aquifer in the qanat water bearing zone, chemical composition of qanat water, absence of well in the qanat catchment and qanat recharge through groundwater infiltration in tunnels of upstream qanats have caused this qanat not to have high discharge decrease. Discharge increase of qanats due to the increase in effective precipitation amount was estimated 4 to 15 percent. Discharge changes amoung studied qanats due to groundwater drowdown in the Gonabad Plain, is not the same, and due to one meter groundwater level drowdown in Gonabad Plain, discharge decrease of qanats estimated 3 to 14 liter per second. With the current groundwater drowdown in Gonabad Plain, qanats will perish during 10 to 180 next years. The electrical conductivity of the groundwater of these qanats varies from 750 to 3900 µmoh/cm. The dominant water types of these qanats are Na+-Mg2+-HCO3- and Na+-Cl-. Neogene deposits (evaporates and marl) are deteriorating the water quality in the east and the electrical conductivity of groundwater of these qanats increased from west to the east in Gonabad Plain. Due to the direct cation exchange, the amount of calcium and magnesium deficit in the samples is proportional to their excess sodium. The dominant hydrochemical processes in the groundwater of the aquifer of qanats are silicate weathering such as sodium plagioclasses and biotite, carbonate and evaporate dissolution, dedolomitization and normal cation exchange. The groundwater of qanats is saturated with respect to calcite and dolomite and undersaturated with respect to halite and gypsum. The 2H and 18O isotopes signatures of qanats in wet seseon and catchment precipitation demonstrate the meteoric origin of the groundwater of these qanats and the flow mechanism is direct infiltration of precipitation before evaporation through fractures in the limestone and sandstone formations at the south of the basin and infiltration of surface water in the coarse grain alluvial cones at the south border of the plain. The groundwater recharge of these Qanats originates from the precipitation of the altitudes 2000 to 2700 m.a.s.l. The groundwater of these qanats has depleted stable isotopes in the wet season due to recharge through the infiltration of precipitation and has enriched stable isotopes in the dry season due to recharge through the return flow of qanats and springs used for agricultural activities in the south of the basin. There are direct relationship between isotopic content of the groundwater of qanats and their length, mother well depth, and distance between mother well and altitudes.