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• A comprehensive comparative empirical analysis on the container shipping network. • Supported by extensive datasets, incorporates the latest development on river basin. • Combine descriptive and explanatory analysis from interdisciplinary approaches. • A large diversity exists in how inland port systems development. The formation of barge networks on rivers and associated inland port systems is subject to a complex set of influencing factors and mechanisms. This paper aims to present a comprehensive comparative empirical analysis focusing on the container shipping (barge) network in the Yangtze and the Rhine. This analysis is supported by extensive datasets on both river basins, incorporates the latest development on both rivers and is grounded on concepts and methods coming from transport geography and economic geography. We find that a large diversity might exist in how inland port systems and related gateway seaports are dealing with cargo flows and supply chains. In view of explaining this diversity, we make a distinction between geographical/nautical aspects, macro-economic factors and institutional/governance factors. In particular, we discuss the role of institutional and governance factors in barge network development by using the concepts of selection, retention and variation. [ABSTRACT FROM AUTHOR]