In recent decades in Romania, no flood management plan has been implemented in natural riverbeds, although there are known areas that face repeated floods such as the Siret River basin. Practically every year, floods produce uncontrolled erosions and landslides in certain areas, followed by the deposition of sediments, usually on agricultural land, compromising crops indefinitely. This paper analyzes the natural transport capacity of the Siret River based on direct measurements and data recorded during the floods of 2005 and 2020. The mathematical model of the sediment transport is presented, starting with the upstream zone, from the confluence with its main tributaries: Bistrita, Trotus, and Cracau. The recorded flood hydrographs are used in this analysis to model the sediment transport for variable flow rates. The upstream flood hydrograph, the steady downstream level, and the initial riverbed cross-sections represent the boundary conditions. The mathematical model is numerically tested for the risk zones by determining the modifications of the riverbed cross-sections. The variation in time of the liquid and solid phases allows the estimation of the longitudinal riverbed shape with the floodable surfaces. To mitigate the effects of floods—and to protect the population, agricultural lands, and environment—some solutions are finally proposed.