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Water is an essential element for agricultural sustainability. In volcanic islands, freshwater sources are limited, challenging the local farming water supply. Rainfall dependence in the Galapagos Islands limits continuous agriculture, and despite using natural water sources, their irrigation quality is little known. This study aimed to carry out a control–diagnosis of irrigation water quality of the natural sources of the four agrarian islands of the Galapagos, considering water quality parameters for the proposal of sustainability strategies in the water and agricultural context. The workflow included (i) freshwater supply situation diagnosis, (ii) physicochemical parameters measurement and hydrochemical characterisation, and (iii) irrigation analysis and sustainability strategies configuration. Results indicated that of the 34 sources analysed, 55.88% are suitable for irrigation and are located in San Cristobal and Santa Cruz. The remaining 44.12% showed problems with parameters such as faecal coliforms, salinity, metals, carbonates, BOD5, and COD above the national permitted limits. Six strategies for water and agricultural sustainability are proposed, including periodic water monitoring, academy–government–community projects, community water board creation, water sowing and harvesting systems, effective management of effluent, and agricultural strengthening. The study guides comprehensive hydric management initiatives to benefit agrarian development and food security, aligning with SDGs 2 and 6. [ABSTRACT FROM AUTHOR]