Water scarcity has become the most significant limiting factor for sustainable economic and social development in the Yellow River Basin (YRB). Despite this, most current studies on water resources in the YRB from a water footprint (WF) perspective have focused on WF measurements and have explored the influencing factors of WF changes in certain industries, while the impact mechanisms driving regional WF changes remain unclear. To bridge this research gap, the WF of nine provinces in the YRB for 2012 and 2017 were quantified using an environmentally extended multi-regional input-output model (EE-MRIO), and the driving forces of regional WF changes were explored via structural decomposition analysis (SDA). The results showed that the WF of the YRB increased by 3.8% to 113.64 billion m3 between 2012 and 2017. With rapid economic development and enhanced inter-regional trade links, the external WF has played an important role in meeting local water demand. Technological advances and production structure adjustments contribute to the reduction of the WF, thus promoting the sustainable use and management of the YRB's water resources. Both consumption patterns and final demand per capita have dominated the YRB's WF growth, particularly in the economically developed middle and lower reaches, where urban household consumption drove the largest WF, accounting for over 40%. Therefore, in the future, continuous optimization of the consumption structure and guidance of green consumption awareness are expected to contribute more to the reduction in WF. The findings of this study reveal the primary causes of WF changes in the YRB and offer a theoretical justification for the formulation of water conservation and sustainable utilization policies.