Spatial–temporal variations in 13 selected water quality parameters from four stations located in the stagnant Haihe River from 2012 to 2014 were analysed. Principal component analysis and cluster analysis were applied. The main latent anthropogenic factors affecting the water quality of Sanchakou, Sixin Bridge, Liulin, and Erdao Gate were combined sewer overflow, organic matter, domestic sewage, and agricultural diffuse source, respectively. External inputs mainly affected quality water in the summer–autumn season. By contrast, intrinsic biochemical processes were highly correlated with water quality in the winter–spring season. Ranges of total nitrogen (TN) and total phosphorus (TP) of four sampling sites measured 1.2 mg/L to 11.4 mg/L and 0.04 mg/L to 2.06 mg/L, respectively. TN/TP (mass ratio) was mainly between 9 and 23, indicating severely eutrophicated mainstream of the Haihe River and sufficient amounts of nutrients for phytoplankton growth and reproduction. Hence, dual nutrients control strategies should be implemented in this stagnant urban river.