Dredging, adsorbent inactivation, and phytoremediation are commonly used to control internal nitrogen and phosphorus sediment loads in eutrophic still-water ecosystems, such as lakes and ponds. However, the effectiveness of these remediation techniques has not been verified for rivers, lakes, and reservoirs with large disturbances. In this study, a calcium-loaded clay granular adsorbent (CRB) was prepared as an alternative to commercial adsorbents, and an experiment was conducted on the ecological restoration effects of both dredging and adsorbent single treatments as well as combined treatments on eutrophic flowing water. The enhancement effect of phytoremediation on the above restoration techniques was investigated. The results indicated that CRB inactivation treatment reduced the phosphorus and turbidity of the water by 63% and 80%, respectively and increased the total nitrogen and permanganate index (CODMn) by 25% and 101% before phytoremediation, respectively compared to the control group. There were no significant differences in the nutrient indexes of the sediment and water between the dredging treatment and the control group, but dredging enhanced the effect of the CRB treatment. Compared with the CRB treatment, the total nitrogen and CODMn of water in the dredging and combined CRB treatments decreased by 13% and 15%, respectively. Phytoremediation significantly improved the effectiveness of the dredging and adsorbent treatments, both individually and in combination. Additionally, there were notable differences in the growth rates of the submerged plants and the contents of different phosphorus speciation among the plant species. Selecting suitable plant species is recommended when implementing phytoremediation methods. This study highlights that the combination of multiple restoration techniques is effective for eutrophic flowing water. The results provide a guide for the ecological restoration of flowing water.