The Danshui River estuarine system is the largest estuarine system in northern Taiwan and is formed by the confluence of Tahan Stream, Hsintien Stream, and Keelung River. A comprehensive one-dimensional (1-D) model was used to model the hydrodynamics and cohesive sediment transport in this branched river estuarine system. The applied unsteady model uses advection/dispersion equation to model the cohesive sediment transport. The erosion and deposition processes are modeled as source/sink terms. The equations are solved numerically using an implicit finite difference scheme. Water surface elevation and longitudinal velocity time series were used to calibrate and verify the hydrodynamics of the system. To calibrate and verify the mixing process, the salinity time series was used and the dispersion coefficient of the advection/dispersion equation was determined. The cohesive sediment module was calibrated by comparing the simulated and field measured sediment concentration data and the erosion coefficient of the system was determined. A minimum mean absolute error of 4.22 mg/L was obtained and the snapshots of model results and field measurements showed a reasonable agreement. Our modeling showed that a 1-D model is capable of simulating the hydrodynamics and sediment processes in this estuary and the sediment concentration has a local maximum at the limit of salinity intrusion. Furthermore, it was indicated that for Q50 (the flow which is equaled or exceeded 50% times), the turbidity maximum location during neap tide is about 1 km closer to the mouth compared to that during spring tide. It was found that deposition is the dominant sediment transport process in the river during spring-neap periods. It was shown that, while sediment concentration at the upstream depends on the river discharge, the concentration in the downstream is not a function of river discharge.