The development of canal automation systems has been made easier by the advancement of science and technology in the modern era. Canal irrigation is a typical method of obtaining water for agricultural use. In this research work, we suggest a flow control system for canal gates based on a microcontroller. The flow control system is composed of an intelligent Microcontroller based Remote Terminal Unit (RTU). The RTU can interface with a variety of sensors, a free local host cloud server, GSM, and numerous modules. A microcontroller-based system is very adaptable and is simple to change locally. Additionally, it can interface with different modules and is less expensive than PLC. The proposed system aims to improve the efficiency of irrigation operations, power consumption, measurement precision, water distribution, and imbalance responses. The remote terminal unit keeps an eye on security, gate opening, solar power status, and water level. Each component of the system is built to run on solar power. In this research, we put more an emphasis on the direct pipe outputs (DPOs), laterals, and distributaries flow monitoring activities. The security, gate opening, and water level are all tracked by the remote terminal unit. The suggested system has the ability to continuously control the flow at the gate location, reducing labor needs and water waste. The flow control system is made up of smaller systems that can operate on their own while yet working as a whole. The technology is very effective and efficient at regulating the water flow in canals, enhancing irrigation methods, and minimizing water waste.