Irrigation enterprises can be evaluated from a perspective of technical and environmental efficiency. This study determines the technical and environmental efficiency in irrigated cotton enterprises. This is achieved by investigating efficiency at cotton enterprise in the case study area of the Mooki Catchment, located in northern New South Wales. Deep drainage loss which contributes to salinity is considered as an environmental detrimental output. Using four different specifications of Data Envelopment Analysis relative efficiency rankings are determined for each agricultural area in the catchment. This result is then compared to biophysical characteristics from previous studies to help identify the particular features of an area which may influence outcomes that are both environmentally sound and economically efficient. With the identification of the most and least efficient cotton irrigating areas in the region, policymakers can construct a relative ranking system to best determine policy directions in order to achieve economic and environmental objectives.