The distribution and productivity of nutrients, eddy formation, energy dissipation, and other ocean properties are influenced by the variability of Western Boundary Currents (WBCs). In the Southwestern Atlantic, the key features are the Brazil-Malvinas Confluence (BMC) and the North of Brazil Current (NBC). This work investigates them using a 20-year high-resolution ocean model simulation with the Modular Ocean Model version 6 (MOM6) 1/14° configuration of the Southwestern Atlantic (SWA). The results reveal a significant deviation in the path and trends of volume transport of the WBCs over the decades. The Brazil-Malvinas Confluence (BMC) region gets saltier and warmer, with increased kinetic energy and transport. Although transport trends in the NBC indicate reduced transport, this results from weaker wind forcing, which reduces the mixing layer depth in the simulation and the subsurface transport in the region. The warming in the Brazil Current region triggers a stronger southward flow, resulting in a southward shift of 0.93° ± 0.08 of latitude/decade in the BMC separation. Working against this flow, the propagation of the Kelvin Waves from the Eastern Pacific Ocean induces a northern shift of the BMC, revealed by topographic Kelvin waves in the spectral analysis. This Pacific-Atlantic inter-basin relation indicated here underscores the importance of propagating Pacific disturbances into the region to maintain the positioning of the BMC and its properties under a warming Atlantic Ocean.