Analytically assessing groundwater quality is indispensable for sustainable use of groundwater and its effective pollution controls. A large volume of groundwater is stored in the Tedori River alluvial fan one of which of the predominant land uses being irrigated paddy fields. Much groundwater under the fan is used for drinking and industrial purposes. For assessing agricultural activities at the paddy and upland fields on groundwater quality during an irrigation period, multiple water quality items were measured in several water types, including groundwater, river water, and paddy water. Water quality indicators, such as major dissolved ions, a number of trace elements, and some isotopes were measured. The concentrations of nutrients and some elements related to the environmental standards indicated that pollution in the groundwater in the fan was not severe. Concentrations of the tracers (Mg, Na, δD, δ18O) in the shallow groundwater were low along the Tedori River and increased with distance from the river; this trend would be caused by dilution effect by the river water. It was also shown that the paddy field also affects groundwater quality by the infiltration of irrigation water.