The effects of multiple piers with 3D geometries on water levels during floods, as well as riverbed fluctuations and local scour after floods were examined via hydraulic model experiments. The Kintaikyo Bridge in Japan, a world-famous historical triple-wooden-arch bridge, was modeled at a scale of approximately 1/276. The number of model piers was set to four, as in the real bridge, and they were 3D printed and installed in the sand layer of an open channel. To provide adequate information on the pier installation conditions and hydraulic response, four cases were studied in the experiments, primarily considering present pier conditions; the previous conditions of the Kintaikyo Bridge were also considered. The experimental conditions in these four cases depended on whether foundations were present, the piers were skewed against the flow center, and the shape was spindle or similar to that of the present case. In the current bridge condition where foundations are present and there is no skew, water level rise, riverbed fluctuation, and local scour were suppressed. Furthermore, the statistical analysis of the results suggested that riverbed fluctuations are more stable after flooding. The two piers with foundations had smaller scour areas than those without. Further, those with foundations generally had lower mean scour at the pier perimeters. Regarding those without foundations, there were no differences in riverbed fluctuations or local scour due to the skewed pier angle. In addition, the representative length of the pier with a 3D geometry was determined by dividing the projected area of the pier below the initial sand surface in the main flow direction by the pier height, and the relationship between the Froude number or the mean water depth and the maximum scour depth was investigated.