Water scarcity for agriculture is one of the most important challenges to improve food security worldwide. In this thesis we study the potential to develop a low-cost controller for a small scale brackish desalination plant that consists of proven water treatment technologies, reverse osmosis, cation exchange, and nanofiltration to treat groundwater into two final products: drinking water and irrigation water. The plant is powered by a combination of wind and solar power systems. The low-cost controller uses Arduino Mega, and Arduino DUE, which consist of ATmega2560 and Atmel SAM3X8E ARM Cortex-M3 CPU microcontrollers. These are widely used systems characterized for good performance and low cost. However, Arduino also requires drivers and interfaces to allow the control and monitoring of sensors and actuators. The thesis explains the process, as well as the hardware and software implemented.