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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. 

Abstract. Particle tracking is widely utilized to study transport features in a range of physical, chemical, and biological processes in oceanography. In this study, a new offline particle-tracking package, Tracker v1.1, is introduced, and its performance is evaluated in comparison to an online Eulerian dye, one online particle-tracking software package, and three offline particle-tracking software packages in a small, high-resolution model domain and a large coarser model domain. It was found that both particle and dye approaches give similar results across different model resolutions and domains when they were tracking the same water mass, as indicated by similar mean advection pathways and spatial distributions of dye and particles. The flexibility of offline particle tracking and its similarity against online dye and online particle tracking make it a useful tool to complement existing ocean circulation models. The new Tracker was shown to be a reliable particle-tracking package to complement the Regional Ocean Modeling System (ROMS) with the advantages of platform independence and speed improvements, especially in large model domains achieved by the nearest-neighbor search algorithm. Lastly, trade-offs of computational efficiency, modifiability, and ease of use that can influence the choice of which package to use are explored. The main value of the present study is that the different particle and dye tracking codes were all run on the same model output or within the model that generated the output. This allows some measure of intercomparison between the different tracking schemes, and we conclude that all choices that make each tracking package unique do not necessarily lead to very different results.