The interaction and mutual influence of water resources, water environment, and water ecology play a crucial role in integrated basin water system planning and the harmonious development of a high-quality economy. In this study, a coupling coordination model was established to assess the development of coupling and coordination among water systems in the Yellow River Basin (YRB). By applying a Vector Auto Regression (VAR) model, it explores the influence mechanisms of key indicators on the sustainable coordinated development of the "Three Waters" system (TWS). Findings from 2005 to 2021 indicate a positive trend in the comprehensive development level of the YRB's TWS. The degree of coupling ranges from good to high-quality, and the coupling and coordination level progresses from near-dysfunctional to highly coordinated. Moreover, the study highlights the alternating effects of 104 yuan of GDP water consumption and wastewater treatment rates on the water resources-water environment system (WRS-WES); Sewage treatment rates and the greening coverage of urban built-up areas have significant and enduring promotional effects on the water environment-water ecology subsystem (WES-WELS). These insights lay the groundwork for the development of innovative ideas and strategies aimed at promoting the integrated and coordinated advancement of the TWS in the YRB.