We investigated the effects of natural environments and human activity on Lake Biwa, central Japan. We determined the concentrations of 19 elements and the compositions of stable S and Sr isotopes in the main tributaries of the lake and compared them with the corresponding values obtained from the lake water during the circulation period. Results of a principal component analysis indicated that the components dissolved in the lower reaches of the tributaries can be divided into group 1 (HCO(3), SO(4), NO(3), Ca, Mg, Sr) and group 2 components (Cl, Br, Na, K, Ba, Rb, Cs). The concentrations of group 1 components were high in the rivers of the southern area, which is urbanized and densely populated, and the eastern area, which consists of plains where agriculture predominates, compared with the rivers of the northern and western areas, which are mostly mountainous and sparsely populated. The concentrations of group 2 components tended to be high in the river water of industrial areas. The delta(34)S values of SO(4) in the river water converged to 0+/-2 per thousand as the SO(4) concentration increased and, excluding the areas where limestone is extensively distributed, as the HCO(3) concentration increased. In particular, both the delta(34)S values (0+/-2 per thousand) and the (87)Sr/(86)Sr ratios (0.7117+/-0.0005) fell within narrow ranges in the small and medium rivers of the eastern plain area, where rice is widely grown. These values agreed respectively with the delta(34)S values of the fertilizers used in the Lake Biwa basin and the soil-exchangeable (87)Sr/(86)Sr in the eastern plain. The characteristics of water quality in the small and medium rivers of the eastern area can be explained by a model in which sulfuric, nitric, and bicarbonic acids generated by the decomposition of agricultural fertilizer and paddy rice selectively leached out alkaline-earth elements adsorbed on the soil and sediments of the plain or dissolved calcium carbonate enriched with Mg and Sr. Compared with tributary waters, the lake water was depleted in NO(3), owing to denitrification, and in Mn, owing to mineralization, which occur under the redox condition of bottom sediments. Excluding NO(3) and Mn, the compositions of both the dissolved elements and the Sr and S isotopes in the water of Lake Biwa can be approximately reproduced by simple mixing of the tributary water, indicating that these components provide effective indices for evaluating the relationship between the waters of the lake and its tributaries.