Abstract: The Pinglu Canal is a backbone project of China’s New Western Land-Sea Corridor and the country’s first river-to-sea canal. Upon completion, the inflow of numerous tributaries will affect the safety of vessel navigation. To mitigate the impacts of tributary confluences on the main canal, it is essential to investigate the hydraulic characteristics of tributary entrances and to develop integrated management strategies. Along the Pinglu Canal, 26 tributaries converge, creating highly complex flow patterns in the confluence zones. Through numerical simulations and physical model experiments, and guided by the principle of harmonious coexistence between engineering and ecology, a set of measures has been proposed, including channel dredging and widening, construction of sloped and multi-stage stilling basins, and the installation of diversion dikes. In parallel, ecological conservation zones have been planned based on the hydrological features of each tributary to achieve both environmental protection and navigational benefits. Hydro-sediment dynamics analyses of five typical tributary confluences—Yawan River, Shabu River, Yuanqin River, Shaping River, and Gaohu River—demonstrate that after regulation, the tributary inflows exhibit stable flow patterns, with cross-flow velocities below 0.3 m/s, meeting navigational safety requirements while also addressing sediment management and ecological enhancement. However, as numerous tributaries of varying scales enter the main canal, their hydrodynamic characteristics differ considerably, resulting in complex confluence flows. In some reaches, abrupt velocity changes, excessive water level drops, excessive cross-flow, and sediment deposition occur, posing serious threats to navigation safety and long-term channel stability. Therefore, systematic research into the hydrodynamic features of tributary entrances and the development of scientifically grounded regulation measures constitute a critical technical challenge for ensuring the smooth operation of the canal. To address the above challenges, this study is based on the practical requirements of the Pinglu Canal project. By employing three-dimensional numerical simulations and related methods, it investigates energy dissipation measures at tributary confluences and their modes of connection with the canal. Combined with sediment yield predictions of the tributaries, the study further examines the sediment transport dynamics at confluence reaches, thereby proposing optimized flow energy dissipation schemes and sediment control technologies to ensure the safe and efficient operation of the canal. Meanwhile, since the realignment sections of tributary inflows involve ecological conservation zones, it is necessary to consider ecological water requirements, hydrological regimes, and water quality conditions in parallel, so as to optimize tributary treatment and enhance both water quality and ecological protection outcomes of the canal. Based on the types and characteristics of tributaries, the study focuses on rational modes of connection between tributary mouths and the canal’s main channel. Five combined regulation approaches are preliminarily proposed, namely sloping, stepped, drop-type, stilling basin, and diversion dam structures. For tributaries whose inflows have a greater impact on navigation in the main channel, physical model experiments have been conducted. This study examines energy dissipation measures at tributary confluences and their modes of connection with the canal. By integrating tributary sediment yield predictions, it investigates the sediment transport dynamics at confluence reaches, and proposes optimized energy dissipation schemes and sediment control technologies to ensure the safe and efficient operation of the canal. The study further highlights that tributary realignment sections often involve ecological conservation zones, where ecological water requirements, hydrological regimes, and water quality considerations must be addressed in parallel. Accordingly, tributary treatments are reasonably optimized to enhance both water quality and ecological protection functions of the canal. For tributaries of different types, a range of measures—such as dredging and widening, sloped stilling basins, multi-stage drop-type stilling basins, diversion dikes, and low weir sediment barriers—are employed, significantly improving flow conditions at the confluence reaches. Throughout the planning and implementation process, the principle of maximizing overall benefits is upheld, giving equal weight to navigation safety, sediment management, and ecological protection. The findings are intended to provide practical experience and demonstration value for the future planning and construction of large-scale canals in China.