Seasonal and spatial variations in major ion chemistry and isotope composition in the rural-urban catchment of the Shigenobu River were monitored to determine the influences of agricultural and urban sewage systems on water quality. Temporal patterns of biochemical oxygen demand (BOD), total nitrogen (TN), total phosphorus (TP), and suspended sediment (SS) were examined at four sites in the rural-urban catchment. Urban land cover, incorporating the effects of increased population, domestic water use, and industrial wastewater, was positively associated with increases in water pollution and was included as an important explanatory variable for the variations in all water quality parameters. Significant trends were found in each parameter. BOD concentrations ranged widely, and were high in urban regions, due to the presence of a waste water treatment plant. TN and SS showed various trends, but did not vary widely, unlike TP. TP concentrations varied greatly, with high concentrations in cultivated areas, due to fertilizer use. Local water quality management or geology could further explain some of the variations in water quality. Non-point-source pollution exhibited strong positive spatial autocorrelation, indicating that incorporating spatial dimensions into water quality assessment enhances our understanding of spatial patterns of water quality. Data from the Ministry of Land Infrastructure and Transport (MLIT) and Environment Ministry (EM) were used to investigate trends in land management. Stepwise regression analysis was used to test the correlation between specific management practises and substance concentrations in surface water and sediment. MLIT and EM data for 1981-2003 showed an increase in TN, TP, and SS concentrations in surface water. High levels of fertilizer in dormant sprays and domestic water use were associated with high pesticide concentrations in water and sediment. This paper presents a novel method of studying the environmental impact of various agricultural management practises and recommends a management strategy that combines the use of reduced-risk pesticides with irrigation and non-irrigation periods in paddy fields. Copyright © 2011 Elsevier Ltd. All rights reserved.