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Abstract A salinity variance framework is used to study mixing in the Salish Sea, a large fjordal estuary. Output from a realistic numerical model is used to create salinity variance budgets for individual basins within the Salish Sea for 2017–19. The salinity variance budgets are used to quantify the mixing in each basin and estimate the numerical mixing, which is found to contribute about one-third of the total mixing in the model. Whidbey Basin has the most intense mixing, due to its shallow depth and large river flow. Unlike in most other estuarine systems previously studied using the salinity variance method, mixing in the Salish Sea is controlled by the river flow and does not exhibit a pronounced spring–neap cycle. A “mixedness” analysis is used to determine when mixed water is expelled from the estuary. The river flow is correlated with mixed water removal, but the coupling is not as tight as with the mixing. Because the mixing is so highly correlated with the river flow, the long-term average approximation M = Q r s out s in can be used to predict the mixing in the Salish Sea and Puget Sound with good accuracy, even without any temporal averaging. Over a 3-yr average, the mixing in Puget Sound is directly related to the exchange flow salt transport.