Abstract: The operational effectiveness of vertical-slit fishways—critical ecological passages enabling fish migration past instream barriers like dams—is severely compromised in sediment-laden rivers. Siltation within pool chambers obstructs migration routes, degrades essential hydraulic habitats, and can ultimately cause functional failure. Previous research has often treated sediment reduction and fish passage facilitation as conflicting objectives. Therefore, this study aimed to design, evaluate, and compare integrated structural modifications for sediment reduction within a vertical-slit fishway, with the explicit goal of synergistically improving both sediment management and fish passage performance. The investigation focused on quantifying the influence of these structures on internal hydraulic characteristics, sediment deposition patterns, and the upstream passage success of fish. The research methodology integrated a three-dimensional (3D) numerical hydrodynamic model with a 1:6-scale physical hydraulic model, constructed based on Froude similarity. The physical model replicated a typical vertical-slit fishway prototype, featuring five consecutive pools. The numerical model was developed using Flow-3D software, employing the standard k-epsilon turbulence model and the Volume of Fluid method for free-surface tracking. It underwent rigorous validation against velocity measurements from the physical model, confirming its accuracy in capturing complex flow patterns. Five distinct sediment-reduction structures were designed and tested: three variants differing in the position and aspect ratio of a bottom orifice integrated into the baffle, and two variants differing in the placement of a cylindrical element within the pool chamber. All experiments maintained identical upstream flow discharge, water level, and sediment concentration boundary conditions. Sediment deposition morphology and volume were meticulously measured after a 1.5-hour test duration. Concurrently, live-fish trials were conducted using juvenile common carp to assess passage effectiveness; the upstream success rate was calculated based on fish successfully navigating from the release point past the first upstream slit within a 10-minute period. The experimental results demonstrated a clear causal relationship between the modified hydraulic environment induced by the structures and the resultant sediment deposition. In the standard fishway design (control case), deposition was concentrated in the low-velocity recirculation zones adjacent to the main flow jet, with a total measured sediment mass of 4.7 kg across the studied pools. All five sediment-reduction configurations successfully modified the flow field and reduced siltation compared to the control. The bottom-orifice structures created a dual-main-jet flow pattern, lowering the peak velocity and turbulent kinetic energy near the vertical slit and redistributing vorticity maxima to the sides of the jets. This resulted in a characteristic π-shaped velocity distribution and altered sediment deposition locations. In contrast, the cylindrical structures induced prominent periodic vortices and a distinct Ω-shaped flow distribution. They significantly enhanced local vorticity and turbulent kinetic energy around the cylinder, which intensified sediment suspension and transport capacity. Among all configurations, the cylindrical structure with a diameter of 0.05 meters, positioned with its centroid 0.10 meters from the upstream baffle and 0.15 meters from the right sidewall, yielded the most substantial sediment reduction. It decreased the total deposition mass by 48.9% to 2.4 kg. Analysis of fish passage data revealed that the structural modifications also influenced fish behavior and success rates. The optimal cylindrical configuration increased the upstream passage success rate of test fish by 16 percentage points, from 64% (control) to 80%. Fish trajectory analysis via hotspot maps indicated that both bottom orifices and cylinders provided additional, alternative migration pathways, increasing the spatial utilization within the pool chambers. The Ω-shaped flow generated by the optimal cylinder created hydraulically diverse conditions that fish could exploit to reduce energy expenditure during ascent. This study conclusively demonstrates that strategically integrating sediment-reduction structures into vertical-slit fishways provides an effective strategy for concurrently managing siltation and enhancing fish passage. Cylindrical elements demonstrated superior comprehensive performance compared to bottom-orifice types, achieving the highest reduction in sediment deposition alongside a significant improvement in fish passage efficiency. The identified optimal cylindrical configuration successfully modified the internal hydraulic regime to create an Ω-shaped flow pattern that promoted sediment transport while offering favorable migration conditions. These findings offer valuable practical insights for the engineering design of sustainable and efficient fishways in sediment-prone river systems. Future research should expand the parametric optimization of such structures, particularly cylinders, and undertake long-term prototype-scale monitoring to validate the durability and ecological benefits of these integrated designs under real-world conditions.