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Abstract Estuarine exchange flow regulates aspects of estuarine biogeochemical processes; however, other tracer‐specific factors can also play an important role. Here, we analyze realistic simulations from a coupled physical‐biological model to quantify volume‐integrated budgets of heat, total nitrogen (TN), and dissolved oxygen (DO) in the Salish Sea and its sub‐basins. Our goal is to evaluate the role of exchange flow in shaping tracer budgets, extending beyond the traditionally emphasized salt budget in estuaries. The three budgets reveal that exchange flow is a consistently important term with a clear annual cycle, but its relative role differs across tracers. For heat, exchange flow‐driven cooling is primarily offset by atmospheric heating, with the two reaching opposing seasonal extremes in summer. For TN, seasonal variability is dominated by exchange flow, whereas the annual mean is dominated by inputs from rivers and wastewater outfalls, and a loss due to benthic denitrification. The DO budget is the most complex: sinks from exchange flow export and respiration are balanced by sources from photosynthesis and air‐sea transfer. Across all three budgets, the sign of the inflow‐outflow tracer concentration differences determines whether exchange flow imports or exports tracers. These concentration differences, which are strongly influenced by coastal wind conditions, set the distinct seasonality of the exchange flow budget terms, while variations in the exchange flow volume transport play a minor role. Our budget quantification approach, based on archived model output, can be extended to other tracers such as carbon and other estuaries for long‐term budget studies.