The Salish Sea is a semi-enclosed estuary whose largest basin (Strait of Georgia) is connected to the north-eastern Pacific Ocean through regions with tight constructions and sills that cause intense tidal mixing. The estuarine circulation is complicated through the tidally mixed region around the San Juan and Gulf Islands (SJGI), which consists of three different straits: Haro Strait, Rosario Strait, and San Juan Channel. Haro Strait, as the largest and deepest of the channels, is the dominant pathway; however, we determine that Rosario Strait also has an important influence in this region. To examine the differences in water transport through the different channels, Lagrangian particle tracking simulations were performed for a 4-year hindcast (from 2018-2022) using the 3-dimensional numerical model SalishSeaCast. While Haro Strait has southward surface flow and northward deep flow, there is primarily southward flow at all depths through Rosario Strait and San Juan Channel. The proportion of the total southward flow through these two channels is higher from May – October and this increase is attributed to the influence of both the Fraser River and the river discharge from Puget Sound. Rosario Strait is the dominant pathway of southward exchange from the Strait of Georgia to Puget Sound, while the majority of deep northward flow to the Strait of Georgia is through Haro Strait.