The middle and lower reaches of the Yangtze River are among China's most economically developed regions, characterized by abundant precipitation and a steady water flow. However, a serious imbalance exists between water resource availability and regional economic development. Nantong City, located on the northern bank of the Yangtze River estuary, exemplifies this issue, facing persistent surface water shortages and heavy reliance on ground-water extraction. To support more rational and scientific water use, this study assesses the sustainability of water resources in Nantong using the ecological footprint method from 2012 to 2021. The results indicate that the overall ecological footprint of water resources in Nantong has remained relatively stable, yet significant disparities exist across districts, primarily due to variations in industrial structure. The ecological carrying capacity and water resource load index fluctuate substantially, with consistent trends across regions that correlate positively or negatively with average precipitation. This suggests that increased rainfall improves ecological carrying capacity while easing water stress. Additionally, the water resource ecological footprint per 10 000 yuan of GDP shows a clear downward trend, reflecting improving efficiency in water use. However, Nantong has remained in an ecological water deficit over the long term, highlighting the need for effective measures to reverse this trend.