In response to the problems of low water resources allocation efficiency and mismatching between water resources utilization and industrial structure in the Dawen River Basin, based on the principle of spatial balance, an analytical framework coupling the input-output model with the system dynamics model was constructed from two dimensions, i.e., the matching between water resources and industrial sectors and the balance of spatiotemporal distribution. The intersectoral virtual water flow patterns were quantitatively identified, and the spatial balance level under multiple objectives was comprehensively evaluated. Through multi-scenario simulation, the water resources spatial balanced development path was revealed. The research shows that from 2012 to 2017, the direct water consumption coefficient and complete water consumption coefficient of all industries in the Dawen River Basin of Jinan City exhibited downward trends. There is room for improvement in the direct and indirect water use efficiencies of industries, including agriculture, forestry, animal husbandry and fishery, mining, and food and tobacco industries. The industrial structure of the basin has shifted from being dominated by agriculture and traditional industries to being led by the tertiary industry. Except for 2014 and 2015 when the water resources balance level was at a generally unbalanced state, the basin as a whole was in a relatively balanced state. The development scheme for new water sources can significantly reduce the water load coefficient and improve the water-soil matching coefficient, and the water-saving level improvement scheme can effectively improve the water use efficiency. The Dawen River Basin should prioritize the reduction of high-water-consuming and low-value-added industries, increase the proportion of services and high-tech industries, jointly achieving ecological protection and green development at the basin scale.