To control pollutants in rivers, we need to have an understanding of the spatial and temporal variations on nutrients and environmental processes in complex river networks. In this study, 177 sampling sites were located in Jinjiang River in 2017, 15 monitoring stations in Jinjiang River from 2011 to 2016 were also collected. According to the data from the monitoring station, the total phosphorus (TP) and total nitrogen (TN) were the dominant contaminants. By analyzing historical water quality data and up-to-date information about the nutrient concentrations, the secondary canals of the Jinjiang River system, most of which were black and odorous, were much more seriously polluted than the main channel and tributaries. Correlation analysis indicated that the NH3, CODcr, TN, and TP had similar sources (R2NH3-CODcr = 0.572, R2NH3-TN = 0.543, R2NH3-TP = 0.537, p < 0.01). The vertical banks of urban rivers and the inadequate and poorly maintained pipe network systems promote deterioration of water quality in these secondary canals. Overall, our results suggest that the river water quality could be improved if the municipal pipe network systems were better maintained and if the vertical banks were transformed into vegetated buffer strips. This study will support initiatives to improve the water quality and function of the river network ecosystem.