Matsuyama in Ehime Prefecture has often experienced droughts and is one of the water-poorest cities in Japan. The purpose of this study is to analyze the effect of well pumping of groundwater on water resources of the watershed from 1950s to 2010s, using the datasets of groundwater level, river discharge, pumping from wells. The major findings are as follows. The groundwater level and river discharge decreased, while the average precipitation did not change in this term. The volume of water to 9 % of the precipitation in this watershed is pumped up from wells along Shigenobu River. WEP (water and energy transfer process) model, a distributed hydrologic model, shows that the well pumping brings the decrease of the groundwater level in the region from down to middle basin of the river. This agrees well with the fact that the drying up of the river is more extensively observed in recent years compared with that in 1950s.