The present work experimentally analyses the flow behaviour near the T-shaped spur dike field with no seepage, 5%, and 10% downward seepage. Experiments were aimed at analysing the channel morphology with different discharges. According to the results, downward seepage movement causes significant modification in the channels bed elevation and the development of scour depth. The maximum scour depth is observed at the edge of the first spur dike facing the flow. The rate of scouring also increases with the effect of seepage. Due to downward seepage, the flow distribution is shifted near the channel bed. However, near the channel boundary attained some velocity, significantly enhancing the sediment transport rate. The wake zone between the spur dikes saw very low-velocity magnitudes of positive and negative values. This reveals secondary current generation inside the loop and cross-stream circulation. With an increment of seepage percentage, the velocity, Reynold shear stress, and turbulent kinetic energy magnitude also rise close to the channel’s boundary.