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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. Sedimentation, which has increased in recent years, is seen as one of the factors contributing to the risk of flooding. The cause of this sedimentation is the subject of the current research. We used the process-based Delft3D FM model to assess the dominant processes in the river and the effects that past interventions along the river and its estuary have had on 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 an increase in tidal asymmetry due to land reclamation and a decrease in episodic flushing by river floods due to upstream dam construction. These processes have induced an increased import of marine sediment potentially responsible for the observed sedimentation. 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.