Abstract A simple sediment transport model was used to reproduce the evolution of sedimentary features in the Tejo estuary over a 50-yr period. The parameterizations of fundamental processes of sediment dynamics such as erosion, deposition and flocculation were evaluated by conducting sensitivity analysis of model simulations to changes in specific parameters and their interactions. The analysis of the sediment budget for model simulations indicated that deposition and erosion mechanisms are sufficient to describe long-term bathymetric changes in the Tejo. The results suggest that erosion is the controlling mechanism in the classic representations of sediment pathways used in the model, while deposition is highly dependent on the prevailing erosion regime. At low to average concentrations of suspended sediments, dynamic feedbacks between deposition and erosion mechanisms control the sediment regime, but for high concentrations (erosional regime) advection determines the net export or accretion in the estuary. The short-term variability of the sediment budget along the longitudinal axis of the estuary is directly related to flocculation effects, which contribute to a significant increase of the instantaneous rates of removal of suspended sediments in the maximum turbidity zone, especially during peak flood and ebb flows. The role of erosion thresholds was also investigated with the purpose of assessing feedback effects among bottom and water-column processes. This study showed that modeling of bottom consolidation processes needed for a realistic representation of the time-space evolution of bed erosion thresholds is essential to replicate sediment processes consistent with in situ observations.