Abstract: The Fenshuiju shoal section in the lower reaches of the Hanjiang River is subject to the combined influence of backwater effects from the Yangtze River and upstream runoff, resulting in significant water level fluctuations and complex flow conditions. In 2022, due to an exceptionally low water level in the Yangtze River, the diminished backwater effect exacerbated local rapid flows and steep longitudinal gradients in the shoal area, posing serious threats to navigational safety. Using a two-dimensional hydrodynamic model, this study investigates the natural flow characteristics and navigation obstructions, proposes targeted channel regulation strategies, and evaluates their effectiveness. Key findings are as follows: (1) The study reach is jointly affected by upstream runoff and the backwater effect of the Yangtze River. During low-flow periods, the weakening backwater effect leads to steepened local gradients—up to 0.45‰ under design water level conditions—with transverse velocities reaching 0.8 m/s. This creates a "waterfall choke point," inducing disturbed flow patterns, increased upstream navigation resistance, and reduced downstream rudder effectiveness. In 2022, the extreme low water level of the Yangtze significantly intensified this choke point effect, leading to deteriorated navigational conditions and highlighting the rare low-flow navigation obstruction. (2) As the Yangtze River water level or runoff increases, the longitudinal gradient exhibits a nonlinear response—first decreasing and then increasing. The elevated water level weakens the constriction effect at the choke point, reduces transverse velocity, and thus improves navigational conditions. (3) The upstream reach of the study section consists of erosion-resistant mudbanks, while the downstream segment comprises more mobile silt deposits. A sharp riverbed elevation drop of up to 4 meters contributes to significant local bed gradients. The heterogeneity of the riverbed intensifies flow disturbances during low-flow periods. (4) In response to low-flow navigation constraints, a regulation scheme involving channel dredging and removal of the shoal at the choke point was proposed. Numerical simulations show that, after implementation, the maximum reductions in longitudinal and transverse flow velocities under design water levels reach 0.4 m/s and 0.6 m/s, respectively. The flow gradient within the navigation channel becomes more moderate, and the alignment between the main flow direction and channel axis improves markedly, effectively mitigating disturbed flow conditions in curved segments. This study demonstrates that targeted regulation measures can alleviate the compounded effects of backwater weakening and riverbed heterogeneity on navigation, offering reference solutions for similar river reaches.