Saltwater intrusion is severely impacting livelihoods and agriculture, a situation particularly evident in Vietnam and especially in the Mekong Delta. Current desalination technologies in the region face persistent challenges related to prolonging membrane lifespan and managing energy consumption. This research introduces a pilot-scale desalination system integrated with Internet of Things (IoT) technology, designed for areas experiencing highly variable salinity levels. The system employs reverse osmosis (RO) membranes for salt removal, along with sensors monitoring pH, turbidity, salinity, and flow rate; all data are collected, wirelessly transmitted via a gateway, and continuously updated to a central server. Over 55 days of operation, feed-water salinity increased gradually from 2 g/L to 13.2 g/L, yet the product water consistently maintained a salinity of 0.0–0.2 g/L, with pH levels stabilizing between 6.4 and 7.3. The clean-water flow rate ranged from 19 to 42 m3/h, demonstrating the system’s adaptability to fluctuating feed salinity. These findings confirm that integrating IoT enables automated control, optimizes operational parameters, and enhances desalination efficiency, paving the way for broader implementation as the demand for clean water continues to rise.