Based on the routine water quality monitoring data of national and provincial surface water monitoring network of Guboshanhou River from 2016 to 2020, the water quality pollution status of Guboshanhou River was comprehensively evaluated by water quality index method (WQI). Based on the results of water quality evaluation, COD_Mn and TP, which have the greatest impact, were selected to carry out intensive monitoring of the Guboshanhou River in October 2020 to investigate and analyze the pollution sources. The results showed that the water quality of Guboshanhou River fluctuated greatly from 2016 to 2020. Rainfall in flood season has a significant effect on the water quality decline. COD_Mn, TP, COD_Cr, fluoride and BOD₅ are the main indexes affecting the water quality of Guboshanhou River. During the intensive monitoring period, COD_Mn and TP concentrations increased by 28.9% and 38.3%, respectively, and the increase rate in Suqian section was significantly higher than that in Lianyungang section. The percentage of tributary with water quality over class Ⅲ was 22.9%, the percentage of that over class Ⅴ was 6.3%. Direct discharge of domestic sewage in some towns and villages and continuous rainfall wash high concentration of pollutants from farmland into river branches, which is the main reason for the decline of water quality.