Inland transport plays a significant role in the lives of the peoples of many countries since it offers many environmental, economic, and social benefits over other modes of transportation. Therefore, many studies have recently been carried out with the purpose of improving the infrastructure of the River Nile in order to increase the annual volume of transported cargoes over a huge network of inland waterways that connect most Egyptian cities. However, further research is required to select a suitable transport system capable of transporting the greatest amount of cargoes through River Nile's very shallow waterways. Thus, in this article, the distinctive characteristics of all river transportation modes employed in Egypt is analyzed and the pusher train barge system has been found to be the most appropriate method of transporting cargoes along waterways with limited water depth. Based on a technical and operational criterion termed transport efficiency, six possible configurations of a proposed pusher train barge system are compared in order to select the most economically feasible configuration to operate along the Cairo-Aswan waterway. For three different loading conditions, this study is carried out with the use of a computational fluid dynamics software package (CFD-FLUENT) and the results are validated.