Irrigation water management has significant economic implications in developing countries like India. While the structural infrastructure has been created with a huge financial investment in these countries, it is vital that appropriate non-structural measures be adopted for efficient water management. Scientific policies of operation of irrigation reservoir systems need to be developed with the aid of mathematical tools and implemented in practice. In this paper, a brief overview of some mathematical tools for irrigation system operation, crop water allocations and performance evaluation is presented, with a discussion on the work carried out in India by the author’s team. Recent tools and techniques of fuzzy optimization and fuzzy inference systems that incorporate imprecision in management goals and constraints and that address the interests of stakeholders are also discussed. Perceptions on issues relating to applicability of the tools to real-life problems, existing gaps between theory and practice and possible hurdles in narrowing such gaps in developing countries are presented