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A bay's capacity to buffer fluvial fluxes between the land and sea is sensitive to hydrological changes that can affect its water renewal rates. In Cartagena Bay, Colombia, pollution issues have been associated with freshwater fluxes which are projected to increase in future years. This has led to plans to reduce freshwater flows by constructing upstream hydraulic doors. Given the influence of freshwater discharge on coastal water renewal, it is important to assess how these upstream changes will affect the bay's hydrodynamic processes. This study calibrated the 3D MOHID Water model, configured with a high-resolution mixed vertical discretization to capture the bay's characteristic processes of vertical stratification and mixing. A Lagrangian transport model was used to analyze the flow of passive particle tracers and calculate water renewal time scales. Mean residence times of 3–6 days and flushing times of 10–20 days for canal water were found, while mean residence times of 23–33 days and flushing times of 70–99 days were calculated for the bay's complete water volume. An assessment of future scenarios showed that increases in freshwater runoff would result in faster water renewal in the bay, while plans to decrease freshwater discharge would result in slower water renewal in the bay. It is therefore imperative that any plans for reducing fluvial fluxes into the bay be accompanied by the control of local pollution sources, which are abundant and could worsen the bay's water quality issues should water renewal times become longer. © 2019 Elsevier Ltd