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Discovering underground water resources remains a vital and inevitable method for optimizing consumption and also maintaining existing resources, not only in the world in general but also in places like Mashhad in particular which faces increasing need for water. Therefore, the present paper aims to identify potential locations for developing karst formations by calculating infiltration percentage of formations. APLIS method, based on GIS analysis, was used to do analytical hierarchical process. Experimental variables assumed to affect infiltration and storage of rain water include altitude, slope, lithology, soil, preferred infiltration sites, and fracture. Information layers for all the above variables were created, and their proportional weight and combinations were specified. Finally, recharge rates of aquifers were calculated and presented in form of maps which also showed the extent of karst formations for various regions. Results let us see that location-specific average of recharge rate for Mashhad formations is 46% in a span of 15–96%. Any increase in infiltration percentage means more karstification in lithology of formations. The ability to map the water resources management and determine the water balance components, including estimating the amount of groundwater resource penetration, and the spatial identification of karst sources compared to other existing methods, is higher. Therefore, the map possesses predictive strength for potential regions of development of karstification. Given the recharge rates for various sites and specified karstic regions, we can anticipate a more efficient management with regard to maintaining water resources and managing consumption. Such management would be more economical and less time-consuming.