The water footprint is the sustainability indicator, which describes direct and indirect water consumption. In the case of a water reservoir, the water consumption is represented by water evaporation from the free surface water. Most reservoirs are built as multipurpose reservoirs. The water losses from the reservoirs should be allocated among individual benefits to avoid distortion of water needs throughout the life-cycle of individual benefits provided by the reservoir. Allocation procedures, i.e. splitting a specific input between multiple outputs, tend to be problematic because different strategies can be used and it is not always possible to clearly determine which strategy is the most suitable. The allocation method significantly influences the assessment of the sustainability of individual benefits provided by the reservoir. In the article, we proposed the categorization of individual allocation strategies, we tested the strategy based on the pairwise comparison of purposes of the reservoir, and carried out an assessment of the variability of results of individual allocation strategies on the pilot case of the Fláje water reservoir. It has been proposed a simplified allocation model using the Analytic Hierarchy Process which is taken as a reasonable compromise between the processing complexity and the need to differentiate between the water reservoir purposes.