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Ensuring food security has become a challenge in Sub-Saharan Africa (SSA) due to combined effects of climate change, high population growth, and relying on rainfed farming. Governments are establishing shared irrigation infrastructure for smallholder farmers as part of the solutions for food security. However, the irrigated farms often failed to achieve the expected crop yield. This is partly due to lack of water management system in the irrigation infrastructure. In this work, IoT-based irrigation management system is proposed after investigating problems of irrigated farmlands in three SSA countries, Ethiopia, Kenya, and South Africa as case studies. Resource-efficient IoT architecture is developed that monitors soil, microclimate and water parameters and performs appropriate irrigation management. Indigenous farming and expert knowledge, regional weather information, crop and soil specific characteristics are also provided to the system for informed-decision making and efficient operation of the irrigation management system. In SSA, broadband connectivity and cloud services are either unavailable or expensive. To tackle these limitations, data processing, network management, irrigation decisions and communication to the farmers are carried out locally, without the involvement of any back-end servers. Furthermore, the use of green energy sources and resource-aware intelligent data analysis algorithm is studied. It is expected that an intelligent data analysis will help to discover new knowledge that support further development of agricultural expertise. The proposed IoT-based irrigation management system is expected to contribute towards long term and sustainable high crop yield with minimum resource consumption and impact to the biodiversity around the case farmlands.