Congestion in ports is a phenomena associated with delays, queuing and extra time of voyage and dwell of ships and cargo at the port, which always occur with unpleasant consequences on Logistics and supply chain. These often translates into extra costs, loss of trade and disruption of trade and transport agreements. In a study to identify the consequences of port congestion on Logistics and supply chain operations in some African ports, this paper has examined the common port congestion scenarios, their dimensions and the various factors that trigger congestion in the ports of Lagos, Durban, Mombasa and the catchment ports of the Suez canal. This paper typically applied the concept of variations in turn-around time of ships and cargo vis-à-vis the port’s capacity and relative efficiency level in order to identify the active factors that cause port congestion in African ports. The results provided some explanations on the consequences arising from these on notable African logistics and supply chain networks. The findings revealed that the bane of congestion in African ports emanates entirely from either planning, Regulation, capacity, efficiency or a combination of these. This paper therefore recommends that African ports should enhance their regulatory mechanisms, then to improve capacity and efficiency level in order to shoulder the ever increasing challenges of port congestion in years ahead.