The Uruguayan continental margin (UCM), located in the Southwestern Atlantic margin’s subtropical region, is positioned in a critical transitional region regarding the global ocean circulation (Río de la Plata (RdlP) outflow and Brazil-Malvinas Confluence), as also reflected in seafloor features (northernmost distribution of a large depositional contourite system and RdlP paleovalley). This complex oceanographic scenario occurring in a relatively small area highlights the advantage of considering the UCM as a natural laboratory for oceanographic research. The present work provides the first conceptual “control” model of the physical drivers (i.e., climate, geomorphology) and main oceanographic processes (i.e., hydrodynamics, sediment, and carbon dynamics) occurring along the UCM, reviewing and synthesizing available relevant information based on a functional integrated approach. Despite the conspicuous knowledge gaps on critical processes, a general picture of the system’s functioning is emerging for this complex biophysical setting. This includes conceptualizations of the actual controls, main processes, feedbacks, and interactions responsible for system dynamics. The structure adopted for developing our conceptual models allows permanent improvement by empirical testing of the working hypothesis and incorporating new information as scientific knowledge advances. These models can be used as a baseline for developing quantitative models and, as representations of relatively “pristine” conditions, for stressors models by identifying sources of stress and ecological responses of key system attributes under a transboundary approach.