With a certain level of buoyancy and velocity that creates silting common in most natural river bodies, the characteristics of varied hydrodynamics and cyclical changes tend to contribute toward the unique silting phenomenon in every river and stream, thus a unique set of problems on the equilibrium of water and silt within each river system. As a result, any attempt trying to divert the water for irrigation or build a structure at the river will invariably alter the river flow. In the mean time, any alteration by diverting some of the water or sand from a river’s original course, or any artificial changes to the water flow or riverbed will also bring forth subtle changes to the diverting point, or even the up- and downstream from such artificial structure in order to reach a new equilibrium between the water and silt. The ramification of silting alone, coupled with problems surrounding changes of the river course over time once a water diversion project is completed, has a detrimental effect toward the routine management of the water diversion project as well as flood protection for such river or stream. It is quite possible that severe silting tends to result at a point where the water is diverted and along the trenches if the location or management of a diversion project should go terribly wrong that could incapacitate the entire project and demand a new site be found where the water can be re-diverted. The study utilizes the NESTARS model for simulating the feature of evolvement on water-borne siting at Nankan Shih, taken into account that the effect of sand carried down from the river’s upstream tributaries has toward the fixed peak flow and the river’s historic flood line at the specific section of the river being simulated at varied intervals of 5, 10 and 20 years, as well as the hydrological changes and silting condition at riverbed near the vicinity where the Nankan retainer dam and related river-crossing structures are located. Under a set of criteria designed to simulate various conditions of flow-speed and delayed peak-flood, the upstream riverbeds above the Nankan Shih’s retainer dam begin to appear with a varied degree of riverbed silting and water hammering, whereas the downstream riverbeds below the retainer dam begin to appear with detectable flushing and a water table that surged and then subsided. Findings concluded from simulating the pattern on the changes of solid particles in diameter along the riverbeds reflect a unique feature how silting varied above and below the retainer dam. The result of the simulation also offer some characteristic changes that the hydrodynamics of water-borne silting above and blow related river-crossing structures along Nankan Shih. Findings of the study also provide a glimpse to the downstream hydrology and features of silting once a retainer embankment is added to a natural river flow, as well as related subjects such as the evolvement of changes in the riverbed after water-drawing embankment has been added to a river, which may provide some reference material in managing trenched irrigation as well as strategizing ways to evaluate and tackle blood protection.