This study investigates the human-water relationship in the endorheic region of Junggar Basin from 1900s-2010s using multi-source data and methods. The results indicate that high-density areas of settlements and water systems have synergistically expanded northward, exhibiting a spatial pattern of phased fluctuation of weakened-enhanced-weakened clustering. There are significant spatial and temporal differences in the evolution of settlement and water system densities across different river basins. Driven by water conservancy modernization, the correlation between settlements and water systems increased significantly during the 1960s, while their natural temporal coupling was weakened. From spatial perspective, the relationship between water systems and settlements presented a synergistic evolutionary process of enhanced agglomeration and scaling. Water conservancy modernization impacted the spatial distribution and interrelationship of water systems and settlements at both oasis and basin scales. The water conservancy modernization initiatives of the 1950s-1960s had profound effects on settlements and water systems, altering hydrological systems and processes, which in turn influenced hydroecology and human settlement environments. These impacts should be considered in oasis ecological construction.