This study examines the distribution of water resources in Protected Areas in Iran and their priority for conservation. The results show that most of the water resources are located in the north and northwest of Iran due to favorable climatic conditions, topography, ambient temperature, and annual rainfall levels. Conversely, the lowest amount of water resources are located in the center and southeast of the country. Water resources were prioritized based on expert ratings of indicators to determine their value for conservation. The wetland with the highest priority for conservation is the Anzali Wetland (Gilan province), which is an international Ramsar Wetland. Conversely, Namak Lake (Qom province) was deemed the least important due to its geographical location, biological sensitivity, and conservation status. Protected Areas were found to support more surface water resources and provide space for the largest percentage of water resources, demonstrating their great value for protecting water resources in Iran. However, the level of protection of these critical resources, although located in Protected Areas, was shown to be insufficient. Therefore, appropriate planning and integrated management approaches are urgently needed to protect water resources and aquatic habitats in Protected Areas in Iran to address the current water crisis.