Modern growth in electronics systems, communication system, and information technology assist in designing canal automation system. The Canal irrigation is tremendously use source of water in irrigation. Microcontroller based system is very flexible for any modification required at site, while this system is cheaper than PLC can interface different modules easily. System involves intelligent Microcontroller based Remote Terminal Unit (RTU) which can communicate different sensors, communication modems, memory, ADC and different modules. In this paper we propose a microcontroller based design for flow control system for gate in canal automation. Flow control system consists of sub systems: RTU, Solar Power system, level measurement system, flow measurement system, gate actuator system, and communication system. In this paper more focus on flow control activities of Distributary, laterals and Direct Pipe Outlets (DPOs). Remote Terminal Unit monitors upstream level, downstream level, downstream flow, power status, gate opening, gate health and security. All system components designed to operates on solar power and battery backup. Conventional operational system has some drawbacks and inaccuracies. Proposed system helps to improve irrigation operational efficiency, power use, accuracy in measurement, water distribution and reactions to imbalance and controls the flow at gate location continuously. This system also helps to reduce water wastage and labour dependency.