Sustainable development associated with the agricultural field of Arequipa, a region in economic growth, is vulnerable to contamination of water resources, putting production systems and food security at risk. Therefore, it is necessary to implement an automated system to control, management, and monitor this vital resource. The proposed work proposed a system to measure water quality monitoring in reservoirs and lakes with high accurate related to global positioning. It includes an embedded computer, multiparameter sonde, and an additional dual GNSS/INS in hardware architecture. The software architecture is fully open-source with compatibility, modularity, and interoperability features between Python and MySQL, allowing data management for real-time data in visual interface on a platform that stores unlimited data logging, monitors and analyzes. The proposed system is validated in an experimental test that measures the water quality of a huge agricultural reservoir, where certified instrumentation is mandatory, as compared to other methods used locally for this action.