With the addition of several thousand passive virtual particles, a well calibrated hydrodynamic model is employed to explore marine connectivity in Spencer Gulf, South Australia, which is a large inverse estuary, on time scales of months to years. Based on a new method of “cumulative flushing time,” findings reveal that Spencer Gulf consists of two distinct regimes. Lower Spencer Gulf is advectively flushed every winter on a seasonal basis. In contrast to this, Upper Spencer Gulf is dominated by diffusive rather than advective processes and experiences flushing over much longer time scales (200–400 days). The physical uniqueness of Upper Spencer Gulf might explain why this region accommodates the largest known giant cuttlefish spawning aggregation in the world. Using a simple approach to mimic the bottom-dwelling behaviour of this species, we were able to reproduce some observed migratory features, but the model fails to predict the return of cuttlefish to their spawning grounds, which remains a puzzle for future studies.