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In many arid countries, rules for the allocation of irrigation water when shortages occur are poorly defined. These weaknesses present a critical constraint to food security and can be a major cause of poverty and hunger. The search for flexible rules for the allocation of irrigation water is especially important in dry regions of the developing world where drought and climate change compound the challenges faced by farmers, extension advisers, water managers and governments. Afghanistan is one country in which inflexible arrangements for allocating irrigation water when drought occurs continue to undermine its food security. This paper develops and applies an empirical framework to evaluate several arrangements for the allocation of irrigation water when shortages occur. The intent of the analysis is to identify a water allocation system for sharing shortages that minimizes the loss in economic benefits and food security by efficiently sharing water supplies when the inevitable drought occurs. An integrated decision framework for water resources is developed that unifies crop, water, and farm data. Several water allocation rules that could increase the flexibility of irrigated agriculture in dealing with water shortages are analyzed for their impacts on farm profitability and food security. Findings show that a proportional sharing of water shortages, in which each canal bears an equal proportion of overall shortages, is the most flexible rule among those analyzed for limiting threats to food security and farm income. This water sharing arrangement is also seen as fair in many cultures and is simple to administer. In the developing world, the design and practical implementation of flexible rules for adapting to periodic water supply changes are important as water shortages become more pronounced in the face of droughts and climate variability. The results provide a framework for identifying, designing, and implementing water allocation rules for food security in the developing world’s irrigated areas.