This study examines the hydrodynamic structure and estuarine-shelf exchange mechanisms at the two primary mouths of the Paranaguá Estuarine Complex (PEC), a multi-mouth estuary system in Southern Brazil. The research defines the hierarchy of controls governing circulation and flow partitioning across tidal and seasonal scales. Tidal forcing is the dominant short-term regulator of exchange volume, establishing an overall ebb-dominant system. Spring tides significantly enhance estuarine flushing, increasing total ebb volume by approximately 40% compared to neap tides. The principal result is the discovery of a complete seasonal reversal of functional dominance between the two mouths that dictates net estuarine-shelf exchange. In summer, the south mouth acts as the dominant export channel (e.g., 66% of total ebb volume), while the north mouth handles imports. This pattern inverts in winter. This asymmetry extends to stratification: the south mouth maintains persistent stratification during summer neap tides (high Richardson numbers, 2.15–2.59), while the deeper north mouth tends toward a well-mixed state during high tidal energy. These dynamics are supported by Coriolis forcing (low Ekman numbers, <0.003) and nonlinear tidal interactions. The major conclusion is that the PEC&apos;s multi-mouth configuration establishes a complementary, asymmetric coupling that is highly sensitive to large-scale seasonal continental shelf dynamics, offering fundamental insight into estuarine-shelf connectivity in complex coastal systems.