In order to ensure the water quality of drainage ditches flowing into the Yellow River to reach the standard and achieve ecological protection and high-quality development of the Yellow River Basin, the water quality index-development (WQI-DET) and principal component analysis index (PCAI) of water quality were used to analyze the spatiotemporal change characteristics of water quality from 2020 to 2022 in the Shizuishan section of the Third and Fifth Drainage Ditches flowing into the Yellow River. Mantel tests and multiple comparisons were employed to explore the driving factors influencing water quality in the drainage ditches, considering both natural and human factors. The results show that the compliance rate for water quality in the Helan section of the drainage ditches is the lowest (57.6% in the Third Drainage Ditch and 69.4% in the Fifth Drainage Ditch). Pollution sources are numerous in the Third Drainage Ditch, making it difficult to manage, while pollution sources are fewer in the Fifth Drainage Ditch, leading to more stable water quality. Irrigation water pollution mainly occurs in the early period of irrigation, while agricultural runoff during the mid-irrigation and winter irrigation periods can have a purifying effect on the river. Many indexes of the Fifth Drainage Ditch vary significantly between the early period of irrigation and other periods ( p ＜0.05). Natural factors have no significant effect on the overall water quality of the drainage ditches, and the local pollution sources are mainly domestic sewage and industrial discharge.