In this paper, we develop a two-stage analytical framework to investigate farming efficiency. In the first stage, data envelopment analysis is employed to estimate the efficiency of the farms and conduct slack and scale economies analyses. In the second stage, we propose a stochastic model to identify potential sources of inefficiency. The latter model integrates within a unified structure all variables, including inputs, outputs and contextual factors. As an application ground, we use a sample of 60 farms from the Batinah coastal region, an agricultural area representing more than 53 per cent of the total cropped area of Oman. The findings of the study lay emphasis on the inter-dependence of groundwater salinity, irrigation technology and operational efficiency of a farm, with as a key recommendation the necessity for more regulated water consumption and a readjustment of governmental subsidiary policies.