Yeast, widely used in wastewater treatment, can make use of organic matter and provide nutrition for other living things. The effect of yeast inoculum addition on the remediation of water and sediment in an urban river was evaluated. In the field test, average removal efficiency of CODCr, NH3-N, and TN was 20%, 25%, and 25%, respectively, in the addition segment after 12 days. After one year, the concentrations of TN and TOC in sediment were not significantly different between the addition and upstream segments. However, species of carbon chains, alkanes with lower boiling points, fatty acids, and esters increased significantly in the sediment after yeast addition, indicating a long-term effect on remediation by increasing biodegradability. Based on two years of long-term monitoring, the total numbers of bacteria, actinomycetes, and fungi in the sediment from the yeast addition segment were greater than those of the upstream segment. The sequencing results showed that the diversity of bacteria in the addition segment was better than that in the upstream segment. In summary, yeast addition had a significant effect on remediation in an urban river by increasing microbial number and diversity and providing a more favourable microbial environment.