The Cost Recovery Principle (CRP) is considered by the European Union (EU) water policy as a substantial requirement for economic efficiency, transparency, fairness, and sustainability in the use of water resources. Nevertheless, the implementation of the CRP by EU Member States has encountered significant challenges, both theoretical and practical, especially regarding the accounting of environmental and resource costs related to water use by the agricultural sector. This paper aims to analyse the application of the CRP to the agricultural irrigation sector in Spain, based on the case study of the Guadalquivir River Basin. To this end, an assessment of the financial, environmental, and resource costs (and the corresponding cost recovery rates) of water services related to the irrigation sector was carried out for this specific river basin. Additionally, this study aimed to offer a much-needed discussion on the agricultural “exceptionalism” phenomenon regarding the application of the CRP at the moment when water and agricultural EU policies are being reviewed to guarantee a more sustainable development of agriculture when using such a strategic natural resource.