Semi-enclosed coastal water systems (SECS) provide essential ecological and economic services. Their sustainable use requires a baseline understanding of the physical dynamics that control their water quality, morphology, and environmental stability. This paper aims to provide an overview of the current state of knowledge on the physical processes in SECS in South America, a megadiverse region that encompasses five of the largest river systems in the world. To achieve this goal, we compiled data from satellite imagery, geological and hydrological maps, and peer-reviewed literature. The information derived from these sources allowed comparisons among systems according to the level of understanding of their local hydrodynamics. Moreover, a recent dynamic classification was employed to identify the main physical forcings of those SECS with sufficient data. 898 SECS were identified in the continent, including deltas, alluvial estuaries, and coastal lagoons. A review of over 500 peer-reviewed publications revealed that 74 systems exhibited enough data to render a dynamic classification possible. In addition, 18 SECS stood out by the advanced understanding of their physical processes. The analysis presented here synthesizes the current understanding and provides an outlook of future challenges. We emphasize the need for continued monitoring of these systems to inform management strategies and mitigate the impacts of environmental stressors.