Observed discharge data covering the last three decades (1980–2009) at 16 rivers (i.e., rivers of Ida, Jinzu, Kurobe, Hime, Seki, Sai, Chikuma, Shinano, Uono, Kiso, Tenryu, Keta, Oi, Kamanashi, Fuefuki, and Fuji) in the Japanese Alps region are analyzed to clarify the elevation dependence of runoff characteristics during the snowmelt season. In the Hokuriku area, where large quantities of snow fall, the center time (CT) of snowmelt runoff tends to be delayed more at rivers with higher catchment-mean-elevations. In addition, the long-term (1980–2009) trend of a forward shift of snowmelt runoff timing becomes more remarkable at rivers in this area, with the exception of Hime River, as catchment-mean-elevation increases. However, the correlation between flowering dates of cherry trees and snowmelt runoff timing is stronger at rivers in the area with a lower catchment-mean-elevation. Consequently, snowmelt runoff at lower elevations in the Hokuriku area is sensitive to year-to-year fluctuations of spring onset, while progressive warming has greater impacts on snowmelt runoff timing at higher elevations, not only in winter to early spring but also in winter to late spring or summer. On the other hand, elevation dependence of snowmelt runoff timing is not detected at rivers in other areas; the runoff characteristics described above are neither clear nor statistically significant at both lower and higher elevations. Our results prove that the hydrological response to global warming is elevation dependent in a snow-dominated region, providing important knowledge for better water-resource management and flood control.