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Irrigated agriculture is a key activity in water resources management at the river basin level in arid and semi-arid areas, since this sector consumes the largest part of the water resources overall. The current study proposes a methodology to evaluate the water footprint (WF) of the irrigated agriculture sector at the river basin level, through a simulation of the anthropised water cycle combining a hydrological model and a decision support system. The main difference from the approaches that have already been used is that the new methodology includes the limitations of the system for the exploitation of water resources where the irrigated areas are located, and it considers the hydrological principles governed by the law of continuity of mass. Water footprint accounting was carried out for the Segura River Basin (South-eastern Spain), applying the methodology proposed and another that is usually applied. The results of the two methodologies were compared, revealing significant differences in the values of the WF, basically due to the blue component. The methodology that is usually applied overestimated the WF of the agriculture in the basin since supply deficits were not taken into account, providing results that would only be possible if there were no spatial or temporal restrictions to water use. So, in order to make the WF indicator useful in water resources management plans, it is necessary to adapt the computations to the main characteristics of the water exploitation system of the whole basin under study, respecting the hydrological principles of the water cycle: regulation and transport infrastructure, the real water resources available and the priority of access to water between concurrent water uses.