The Kitimat Fjord System in the northern British Columbia coast features a network of deep channels, islands, and shallow sills. In particular, the fresh water leaving Gardner Canal bifurcates at a triple junction: (1) north through a shallow sill (100‐m deep) to Devastation Channel and then out through Douglas Channel and (2) west along Verney Passage then passing over a shallow sill (35 m) to Wright Sound. The partitioning of the fresh water leaving Gardner Canal has substantial implications for interpreting estuarine circulation and water exchange of the system. In this study, the partitioning of the fresh water at the triple junction is quantified by using observations and a circulation model. The model is based on FVCOM with ~200‐m horizontal resolution in the narrow channels and forced by tides, winds, and river discharges. The remotely sensed freshwater plume, surface drifter trajectories, and temperature profiles suggest that the fresh water from Gardner Canal contributes to the estuarine circulation in the Douglas Channel. A passive tracer evolving with the advection and diffusion processes in the circulation model is used as a proxy to quantify the freshwater transport. The results show that the majority of low salinity water leaving Gardner Canal at the triple junction flows northward into the Douglas Channel through the Devastation Channel and the synoptic variability of the freshwater partition is modulated by strong wind events. A synthesis of various circulations in the abovementioned connecting channels around the Hawkesbury Island indicates a net anticyclonic circulation.