The Xiao Bei mainstream, located in the middle reaches of the Yellow River, plays a vital role in regulating the quality of river water. Our study leveraged 73 years of hydrological data (1951–2023) to investigate long-term runoff trends and seasonal variations in the Xiao Bei mainstream and its two key tributaries, the Wei and Fen Rivers. The results indicated a significant decline in runoff over time, with notable interannual fluctuations and an uneven distribution of runoff within the year. The Wei and Fen Rivers contributed 19.75% and 3.59% of the total runoff to the mainstream, respectively. Field monitoring was conducted at 11 locations along the investigated reach of Xiao Bei, assessing eight water quality parameters (temperature, pH, dissolved oxygen (DO), chemical oxygen demand (COD), ammonia nitrogen (NH3-N), total phosphorus (TP), permanganate index (CODMn), and 5-day biochemical oxygen demand (BOD5)). Our long-term results showed that the water quality of the Xiao Bei mainstream during the monitoring period was generally classified as Class III. Water quality parameters at the confluence points of the Wei and Fen Rivers with the Yellow River were higher compared with the mainstream. After these tributaries merged into the mainstream, local sections show increased concentrations, with the water quality parameters exhibiting spatial fluctuations. Considering the mass flux process of transmission of the quantity and quality of water, the annual NH3-N inputs from the Fen and Wei Rivers to the Yellow River accounted for 11.5% and 67.1%, respectively, and TP inputs accounted for 6.8% and 66.18%. These findings underscore the critical pollutant load from tributaries, highlighting the urgent need for effective pollution management strategies targeting these tributaries to improve the overall water quality of the Yellow River. This study sheds light on the spatiotemporal changes in runoff, water quality, and pollutant flux in the Xiao Bei mainstream and its tributaries, providing valuable insights to enhance the protection and management of the Yellow River’s water environment.