Population growth, urbanization, and the intensification of climate change have placed additional pressure on limited freshwater resources, especially in arid and semi-arid regions. In such circumstances, the lack of usable water resources has become one of the fundamental challenges in the path of sustainable agricultural development and ensuring food security in these regions. Therefore, the use of alternative sources, especially unconventional waters such as treated wastewater, agricultural drainage, treated industrial wastewater, and saline or brackish waters, as an effective and complementary solution to compensate for water shortages, has increasingly attracted the attention of researchers, water resource managers, and policymakers in recent years. This article aims to provide a comprehensive analysis of the capacities, challenges, and solutions for effective exploitation of unconventional waters in water resources management and promoting sustainable agriculture in arid and semi-arid regions. First, different types of unconventional waters and their quality characteristics are introduced, and then the technologies used in purification, safe application methods, and the health, environmental, and economic impacts of exploiting these resources are examined. In addition, successful experiences at the national and international levels have been analyzed, and the role of macro-policies, legal frameworks, and stakeholder participation in the optimal implementation of these strategies has been considered. The results of this research can be used as a basis for developing policies and implementation plans for the sustainable use of alternative water resources in critical climate conditions. The results of this study show that the principled, targeted, and standard-based use of unconventional water, while reducing pressure on conventional water resources, can pave the way for improving water productivity, increasing the resilience of agricultural production systems, and achieving sustainable development in water-scarce regions.