Inland waterways are one of the most environment-friendly and cost-efficient means of transportation. A fairway with a stable width and sufficient water depth throughout the year is essential for sustainable inland navigation. The Inland navigation route has sections with dynamic hydrodynamical and morphological hotspots like river confluence. The safety of navigation and maintenance of a fairway are aspects that have yet to be thoroughly examined at the river confluence. In the present study, experiments are conducted to investigate the hydro-morphodynamics changes with and without river training structure (Spur dike) under varying flow conditions. The experiments without spur dike study the distribution of cross-currents, sediment bar characteristics, and flow turbulence. The second series of experiments with different head-shaped (Straight, T, and L) spur dikes focus on optimizing the arrangement to ensure a stable fairway with adequate clearance space. It has been observed that the T-head spur dike outperforms the straight and L-head dikes in effectively managing morphological features and limiting the cross-current influence in the lateral and longitudinal extent. The optimized configuration (θd-Leff-Ld-L’) with values (900-0.2WL-6Leff-1Leff) (Where θd is the dike angle, Leff is the effective length, Ld is the dike location, and L' is the wing length) results in substantial reduction of 43.4% in bar width (Wb), 18.64% in bar height (Hb), and 57.69% in bar volume (Vb). It also reclaims 62% of the cross-current influenced zone by diminishing longitudinal (Lc) and lateral (Wc) extents by 33.9% and 50%, respectively. The study investigates surface and cross-sectional flow patterns and their turbulent characteristics, influencing bed morphological changes. Furthermore, a regression equation is proposed using the experimental data to predict the blockage induced by sediment bar formation.