The inverse relationship between water and sediment is hindering the regulation of sediment in silt-laden rivers. Under natural conditions and insufficient water flow, sediment deposits along river channels, resulting in the accumulation of suspended river sediments above the ground level on both sides of the river. Then, during flooding, dam collapse and overflow can easily occur, threatening the life of residents in floodplain. The operation of upstream reservoirs to maximise the sediment transport capacity of downstream rivers into the sea is deemed the best strategy for the management of silt-laden rivers. However, as incoming water and sediment form a dynamic system, optimising the operation mode of reservoirs has become the most severe challenge in the field. This study proposes a method to remodel the water–sediment relationship of natural rivers by optimising the reservoir operation. First, data were collected and analysed to investigate sediment transport in the downstream river channel and the response relationship between erosion–deposition. Then, an empirical equation for calculating the desired incoming sediment was derived, and the threshold for sedimentary transport balance in the lower reach of silt-laden rivers was determined through mathematical modelling. Finally, the reservoir operation mode was optimised within the threshold range to study the discharge process of the reservoir with the highest sediment transport efficiency downstream. The Yellow River in China exhibits the highest sediment concentration worldwide and was used as a case study to verify the practicability of the proposed method. The critical threshold for sediment transport balance in the lower Yellow River was determined to be 250 million tons. The results demonstrate that the proposed method improved the sediment transport capacity of the lower reaches of the Yellow River. Moreover, it reduced the siltation of the XiaoLangDi Reservoir and the lower reaches of the Yellow River. The XiaoLangDi Reservoir can be jointly operated with the Guxian Reservoir, which is under construction and is expected to maintain the bankfull discharge of the lower reaches of the Yellow River at 4000 m³ for a long time. The optimisation process described in this study can be used to improve the management of silt-laden rivers.