The Bras d'Or Lakes (BdOL) is a land-locked estuarine system in central Cape Breton Island. Nova Scotia, Canada. Recent outbreaks of waterborne diseases at several sites in the BdOL have decimated shellfish populations and threaten its unusual biodiversity. Assessing the potential for spread of invasive pathogens is a priority for management. A nested-grid hydrodynamic modeling system is used to simulate the three-dimensional (3D) circulation and temperature-salinity distributions for summer 1974, when currents and hydrographic measurements suitable for model calibration were made at several locations. The modeled 3D velocity fields are then used in Eulerian-Lagrangian transform to study the spatial patterns of retention and dispersion of passive particles, as a proxy for the spread of disease by water flow in the estuary. Probabilities of transfers (connectivity) among 10 sub-domains of the BdOL are calculated from the statistics of the 3D particle trajectories and portrayed in a transition matrix. The model results demonstrate that the hydrodynamic connectivity among the several small bays in the western portion of the BdOL (ranging from 0.1% to 13.5%) is much weaker than those among the main basins (16% to 62.4%) at monthly time scales. Restriction by narrow passages between the small bays and the main basins reduce connectivity among populations and their habitats, but the effect is partially offset by density-driven flows associated with freshwater inputs at the land boundaries. The model can be used to guide epidemiological surveys and generate testable hypotheses of disease spread and species invasions within the ecosystem.