To clarify the pathways and origins of dissolved nitrate (NO3) in rivers flowing into Lake Biwa, Japan, three types of coordinated surveys of concentrations and isotope compositions of NO3- were conducted: (1) synoptic river sampling of 32 representative inflow rivers, (2) two rivers in catchments with different land uses, and (3) headwater catchment samplings. The data set used in this paper is the first comprehensive collection of isotopic composition of NO3- in rivers of a large-scale basin in Asia. While the NO3- spatial concentration pattern showed significant seasonal variation, the spatial pattern of the delta N-15 of dissolved NO3- (delta(1)5N(NO3)) was more consistent throughout the year. The delta N-15(NO3) was significantly positively correlated with the population density of each catchment. A mass balance model assuming the delta N-15(NO3) and the flow rate of sewage effluent was developed. The model simulated the relationship between the population density and the delta N-15(NO3) reasonably well, suggesting that the dominant source contributing to the increase in delta N-15(NO3) was the sewage effluent. The spatiotemporal distribution of delta O-18(NO3) suggested the possibility of the addition of atmospherically derived NO3- through precipitation and was indicated by the hydrological pathways for NO3- exports in different land uses. In forest-dominated catchments with natural drainage systems, a slightly elevated delta O-18(NO3) signal remained in the stream water even during base flow conditions. This study demonstrated that multiscale, multi-isotopic investigation is a promising strategy for describing the spatial distribution of NO3- sources synoptically and is useful for evaluating the influences of land use change.