Nature-like fishway arrangements are commonly used because these structures imitate the characteristics of natural rivers and effectively allow fish to migrate past river sections blocked by hydraulic structures. In this paper, physical models were analyzed, and the velocity distributions of two different fishway structures (Types I and II) were compared. Results showed that the maximum mainstream velocity of the Type I structure was 5.3% lower than that of the Type II structure. However, the average mainstream velocity of the Type I structure was 21.1% greater than that of the Type II structure. The total per-cycle length of the mainstream path in the Type II structure was 2.1 times greater than that of the Type I structure, which indicated that the length of the mainstream path was somewhat proportional to the average velocity of the mainstream. When the flow rate was kept constant, increases in the velocity of the main flow associated with changes in the internal structure of the fishway decreased the average velocity of the main flow, while decreases in the total length of the flow path led to increases in the average velocity of the main flow. Due to frictional head loss along the fishway and local head loss, as well as the overlaps between these factors, the overall flow rate gradually decreased every cycle, despite periodic fluctuations.