In rivers where farmlands and livestock farms are scattered throughout the watershed, anthropogenic nutrient loading may affect not only water quality but also the river ecosystem. In this study, we evaluated the effects of anthropogenic nutrient loading on the material cycle and food web in the Yukiya River and Setsukinai River using carbon and nitrogen stable isotope ratios (δ13C and δ15N). We collected macroinvertebrates and food sources (attached algae, leaf, suspended particle organic matter (SFPOM) and benthic particle organic matter (BFPOM)) from study sites. The results of δ13C and δ15N suggested the impact of anthropogenic nutrient loading at all sites except the upstream of the Setsukinai River.The stable isotope two source mixing model based on δ13C revealed that macroinvertebrates consumed mainly attached algae. The significant positive correlation between the δ15N of attached algae and the δ15N of each feeding function groups suggested that a food web based on attached algae was constructed in the study rivers. Therefore, it is suggested that the effects of anthropogenic nutrient loading are propagated to macroinvertebrates through attached algae and FPOM derived from attached algae, and that these effects extend downstream to the dam through eutrophication of the dam lake.