Water scarcity and land degradation increases led to a sharp rise in input resource’s costs. These developments make it increasingly difficult for agricultural farms to produce according to the demand for food and other commodities, especially owing a rapid population growth. The present study aims to focus on scarce resource use in the agricultural production of the Zarafshan valley by means of the efficiency analysis. A DEA model is estimated to investigate the farm level efficiency levels with respect to the use of the limited resources available to the farmers. By the application of linear programming methods a ‘best practice frontier is estimated’, classifying farms on the frontier as efficient and others as inefficient with respect to different scales. Technical and allocative efficiencies are calculated relative to the frontier. Results shows input resources are not used efficiently and a great majority of farms could effectively reduce considerable amounts of input use by still producing the same output.