As urbanization progresses and city populations grow, river-crossing tunnels assume a crucial role in transportation networks, with the maximum scour depth constituting a critical parameter influencing tunnel safety. Using Line 6 of the Nanning Metro in Guangxi, China as a case study, a two-dimensional hydrosediment mathematical model was employed to investigate variations in maximum bedrock scouring. This study introduces the concept of critical frequency floods and compares it with urban flood control standards to determine the appropriate flood frequency for calculating maximum bedrock scour depth. The impact of bed sediment particle size on maximum scour depth is quantified, revealing a decrease in scour depth of 0.3 to 0.6 m for every 1 mm increase in particle size. The relationship between bed sedimentation and the Froude number demonstrates an upward-opening parabolic symmetry: lower Froude numbers correspond to relatively stable beds, while higher numbers correlate with an increased amplitude of bed erosion or deposition. The curve’s nadir identifies the critical threshold of the Froude number, facilitating calculation of the channel’s critical water depth. In practical engineering applications, a bed under conditions of critical water depth tends to be more stable, thereby favoring the selection of sites for river-crossing tunnels.