Water, one of the most valuable resources, is underutilized in irrigated rice production. The yield of rice, a staple food across the world, is highly dependent on having proper irrigation systems. Alternate wetting and drying (AWD) is an effective irrigation method mainly used for irrigated rice production. However, unattended, manual, small-scale, and discrete implementations cannot achieve the maximum benefit of AWD. Automation of large-scale (over 1000 acres) implementation of AWD can be carried out using wide-area wireless sensor network (WSN). An automated AWD system requires three different WSNs: one for water level and environmental monitoring, one for monitoring of the irrigation system, and another for controlling the irrigation system. Integration of these three different WSNs requires proper dimensioning of the AWD edge elements (sensor and actuator nodes) to reduce the deployment cost and make it scalable. Besides field-level monitoring, the integration of external control parameters, such as real-time weather forecasts, plant physiological data, and input from farmers, can further enhance the performance of the automated AWD system. Internet of Things (IoT) can be used to interface the WSNs with external data sources. This research focuses on the dimensioning of the AWD system for the multilayer WSN integration and the required algorithms for the closed loop control of the irrigation system using IoT. Implementation of the AWD for 25,000 acres is shown as a possible use case. Plastic pipes are proposed as the means to transport and control proper distribution of water in the field, which significantly helps to reduce conveyance loss. This system utilizes 250 pumps, grouped into 10 clusters, to ensure equal water distribution amongst the users (field owners) in the wide area. The proposed automation algorithm handles the complexity of maintaining proper water pressure throughout the pipe network, scheduling the pump, and controlling the water outlets. Mathematical models are presented for proper dimensioning of the AWD. A low-power and long-range sensor node is developed due to the lack of cellular data coverage in rural areas, and its functionality is tested using an IoT platform for small-scale field trials.