The current situation of structural water scarcity due to the rise in demand, the reduction in supply as a consequence of climate change, increasingly frequent drought periods, and overall quantitative pressure on water resources creates a need for economic instruments to reduce the amount of water used, especially in the agricultural sector. Thus, water pricing and allocation quotas (proportional reduction of allocations) may be suitable tools to reduce demand or allocate scarce water resources. For a comparative analysis of the performance of these two measures, a Positive Mathematical Programming model has been developed, using the Guadalquivir River Basin as a case study. Additionally, the analysis takes into account the revenue generated from water pricing and the marginal cost of public funds. The results indicate that, from the farmer’s perspective, quotas result in smaller losses than water pricing. However, when considering water pricing along with the revenue generated from this measure, this mechanism would be more beneficial for society as a whole, since the taxes collected could be used for other purposes, albeit with efficiency losses measured by the marginal cost of public funds and the excess burden of taxation.