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The Equatorial Daule and Babahoyo rivers meet and combine into the tidal Guayas River, which flows into the largest estuary on the Pacific coast of South America. The city of Guayaquil, located along the Guayas, is the main port of Ecuador but, at the same time, the planet's fourth most vulnerable city to future flooding due to climate change. Fluvial sedimentation, which has increased in the recent years, is seen as one of the factors contributing to the risk of flooding. The planning and design of effective mitigation measures requires a good understanding of the causes which have led to the current hazards. In this study, the process-based Delft3D FM model was used in order to explain the dominant processes in the river and the effects that past interventions along the river and its estuary have had in the overall sediment budget. Additionally, a simulation including sea level rise was used in order to understand the possible future impact of climate change on the sediment budget. Results indicate that the increased import of marine sediment is the result of the recent increase in tidal asymmetry due to land reclamation and a decrease of episodic flushing by river floods due to upstream dam construction. This is in contrast with the local perception of the problem, which ascribes sedimentation to deforestation in the upper catchment. Only the deposition of silt and clay in connected stagnant water bodies could perhaps be ascribed to upstream deforestation. [ABSTRACT FROM AUTHOR]