This article provides a comprehensive overview on cooperative control methods for waterborne transport. We first proposed a hierarchical architecture of cooperation in the waterborne transport systems. Three layers of cooperation are identified according to the range of communication and cooperation, i.e., the individual layer, the local layer, and the network layer. The individual layer is the basis layer where a controller controls the dynamics of an individual vessel. The local layer considers the vessel-to-vessel (V2V) and vessel-to-infrastructure (V2I) interactions. The network layer considers not only V2V and V2I interactions but also the interdependence of the interconnected infrastructures, i.e., infrastructure-to-infrastructure interactions. Existing research for cooperation at each layer is reviewed, and the main research gaps are provided.