<p>The integration of shaft hydropower plant (SHPP) modules into existing weir structures offers a compact and potentially environmentally compatible solution for low-head hydropower generation. However, site-specific geometric constraints and operational variability can substantially affect intake hydraulics and, consequently, ecological performance. This study presents a structured three-dimensional CFD-based hydraulic optimization framework applied to the At-Bashy demonstration site (Kyrgyzstan), representing a SHPP configuration integrated into an existing gated weir. Nine intake configurations were systematically evaluated by varying trash rack length (6–8 m) and submergence above the rack (2.00–2.85 m) while maintaining constant turbine and bypass discharges. Fish-relevant hydraulic indicators were quantified within defined near-rack volumes of interest using time-averaged metrics. In addition to mean velocity components, tail-based indicators of extreme downward-directed velocities and statistical measures of free-surface variability were assessed. Results demonstrate that increasing submergence consistently reduces extreme downward velocities and homogenizes the near-rack flow field. Increasing rack length primarily lowers average downward deflection. Strong upstream flow asymmetry caused by geometric constraints induces localized flow separation and heterogeneous vertical flow velocity cores, highlighting the importance of site-specific hydraulic assessments. A rack length of 7 m combined with operational submergence levels between 2.35 m and 2.85 m provides a balanced compromise between ecological performance and structural-economic feasibility. The study confirms that SHPP intake optimization cannot rely on generalized empirical rules but requires site-adapted numerical evaluation. The presented CFD-based framework provides a transparent and transferable methodology for hydraulic optimization of SHPP intake configurations.</p>