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In this paper we assess the economic impact of evaporation losses from great dams (GDs) and on-farm agricultural water reservoirs (AWRs) in the semi-arid Segura River basin, SE Spain. Evaporation losses from water reservoirs reduce the high water use efficiency reached in agriculture by means of other techniques such as well-built water pipes or drip irrigation and have a substantial economic impact. Evaporation losses have been calculated using Class-A pan evaporation data and pan coefficients, whereas their economic impact has been assessed using an economic mathematical programming model that simulates land and water allocation in the different irrigated areas of the basin. Our results show that annual evaporation from GDs and AWRs represents 8.7% of the water currently available for irrigation in the Segura basin. The economic impact of such losses has been estimated in a reduction of 6.3% of the value of agricultural production and 5.4% of the farm net margin. As less water is effectively available for farmers the basin’s irrigated area is reduced in a 7.5%. This impact is greater, in both absolute and relative terms, in the areas accommodating the most intensive and profitable irrigated agriculture. The applied methodology and results could be useful to regional water agencies and collective irrigation schemes for future planning and management, including the assessment of alternatives for reducing evaporation from reservoirs.