Rice farming threatens freshwater resources, while also being increasingly vulnerable to drought due to climate change. Rice farming needs to become more sustainable and resilient to climate change by improving irrigation drainage systems. Small water bodies, used to store drainage water and supply irrigation in traditional rice farming systems have gradually been abandoned in recent decades. This has resulted in a higher water footprint (WF) associated with rice farming due to increased freshwater usage and wastewater release, also leaving rice production more vulnerable to extreme weather events. Here, we propose how protecting and reactivating small water bodies for rice irrigation and drainage can decrease rice production WF in China by 30%, save 9% of China’s freshwater consumption, increase irrigation self-sufficiency from 3% to 31%, and alleviate yield loss in dry years by 2–3%. These findings show that redesigning rice irrigation drainage systems can help meet water scarcity challenges posed by climate change.

Climate change, population growth, and agricultural intensification are increasing nitrogen (N) inputs, while driving the loss of inland water bodies that filter excess N. However, the interplay between N inputs and water body dynamics, and its implications for water quality remain poorly understood. Analyzing data from 1995 to 2015 across China, here, we find a 71% reduction in the area of small (<10^4.5 m²) water bodies (SWB), primarily in high-N-input agricultural regions. Preferential loss of SWBs, the most efficient nutrient filters, places 42% of China at high water quality risk due to increasing N inputs and declining SWB density. Currently, N removal by water bodies is 986 kilotonnes year⁻¹, but restoring 2.3 million hectares of SWB could increase removal by 21%, compared to just 5% for equivalent restoration of large water bodies. Targeted SWB restoration is crucial for improving water quality and mitigating N pollution in China.

Sewage leakage, including uncollected, collected but exfiltrated, and collected but discharged with stormwater in combined sewer overflows, becomes a key challenge to clean water around the world. This study proposed a mass balance model to quantify sewage leakage and analyzed its influencing factors. Approximately 56% (53%–59%) of domestic total nitrogen loads in the Yangtze River basin of China leak out without treatment, two-thirds are exfiltrated or overflowed, significantly impacting receiving water quality. Cities with higher precipitation have greater leakage, indicating overflows are important. Pipe density has limited impact, showing higher importance of pipe quality over quantity. The per capita leakage rate first increases with city size and then decreases, showing the economies of scale. Yet uneven distribution of population and economy within megacities leads to greater leakage. Hence, separated sewage systems of rainwater and wastewater, regular maintenance and adapting centralized and decentralized systems are recommended, tailored to city-specific leakage characteristics.