Abstract. Numerous studies have quantified stream–groundwater interactions using geochemical or environmental tracers. However, in watersheds where water is extensively used for rice paddy irrigation, uncertainties in estimation remain due to kinetic fractionation of stable isotopes during evaporation from ponded paddies and seasonal variations of the isotopic composition of recharged water. In this study, we used three different methods (streamflow observation, stable isotopes of water, and Sr isotopes) to quantify groundwater discharge to streams in a watershed substantially impacted by rice paddy irrigation in central Japan. We conducted point- and watershed-scale observations of surface water, soil water, groundwater, and ponded water in rice paddies and examined changes in these isotopic compositions. Point-scale observations revealed that Sr isotopes were more appropriate for quantification because the Sr isotopes in groundwater was significantly different from surface water and less variable in time compared to water isotopes. At watershed-scale, isotopic compositions of stream water changed linearly from upstream end to downstream end, suggesting streamflow consisted of two endmembers. We then quantified groundwater discharge to the stream based on measurement of streamflow and surface lateral inflow/outflow during both irrigation and non-irrigation periods. This water balance method yielded large uncertainties in the estimation due to errors in streamflow measurement, while Sr isotopes provided well constrained estimates during both irrigation and non-irrigation periods. The ratios of groundwater to the stream, estimated from Sr isotopes, was in the range 7–86 % during the irrigation period and 38–66 % during the non-irrigation period. Stable isotopes of water also provided good estimates during the non-irrigation period but underestimated groundwater discharge during the irrigation period due to the ill-defined groundwater end member. The use of Sr isotopes has the potential to aid in quantification of temporal variations in groundwater discharge and to provide important information for water resource managers.