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Irrigation plays a pivotal role in Southern Europe, and its importance is expected to further increase due to rising climatic variability. Concurrently, the European Water Framework Directive (WFD) mandates the safeguarding of water bodies and the implementation of incentive pricing strategies to promote efficient water management. Within this context, Irrigation Scheduling Decision Support Systems (IS-DSS) could contribute to the achievement of these objectives, although there are still obstacles to their adoption due to uncertainties regarding their potential benefits. This paper aims to derive a pricing model that reflects actual water use through the adoption of an IS-DSS. The innovation of this study lies in showing that adopting an IS-DSS to reduce irrigation volumes can potentially lower concession fees in collective irrigation systems. Thus, it contributes to the fulfilment of the WFD’s objectives regarding incentive water pricing. Notably, the tool is evaluated using the case study of a farm located in the Mediterranean region. The results demonstrate the dual benefits of IS-DSS adoption: on the one hand, it helps preserve water resources with a 24% reduction in irrigation volumes; on the other, it decreases irrigation costs by 20% at the farm level and by 9.4% at the irrigation district level. Therefore, the presented study provides insights into the potential of IS-DSS to enhance water pricing policies to promote efficient water management in Southern European agriculture in alignment with the WFD requirements.