AbstractThe quantitative evaluation of the effects of bedrock groundwater discharge on spatial variability of stream dissolved organic carbon (DOC), dissolved inorganic nitrogen (DIN) and dissolved inorganic phosphorous (DIP) concentrations has still been insufficient. We examined the relationships between stream DOC, DIN and DIP concentrations and bedrock groundwater contribution to stream water in forest headwater catchments in warm‐humid climate zones. We sampled stream water and bedrock springs at multiple points in September and December 2013 in a 5 km2 forest headwater catchment in Japan and sampled groundwater in soil layer in small hillslopes. We assumed that stream water consisted of four end members, groundwater in soil layer and three types of bedrock groundwater, and calculated the contributions of each end member to stream water from mineral‐derived solute concentrations. DOC, DIN and DIP concentrations in stream water were compared with the calculated bedrock groundwater contribution. The bedrock groundwater contribution had significant negative linear correlation with stream DOC concentration, no significant correlation with stream DIN concentration, and significant positive linear correlation with stream DIP concentration. These results highlighted the importance of bedrock groundwater discharge in establishing stream DOC and DIP concentrations. In addition, stream DOC and DIP concentrations were higher and lower, respectively, than those expected from end member mixing of groundwater in soil layer and bedrock springs. Spatial heterogeneity of DOC and DIP concentrations in groundwater and/or in‐stream DOC production and DIP uptake were the probable reasons for these discrepancies. Our results indicate that the relationships between spatial variability of stream DOC, DIN and DIP concentrations and bedrock groundwater contribution are useful for comparing the processes that affect stream DOC, DIN and DIP concentrations among catchments beyond the spatial heterogeneity of hydrological and biogeochemical processes within a catchment.