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Traditional agricultural practices in the Huang-Huai-Hai Plain have led to a decrease in groundwater level, coupled with frequent extreme rainfall in recent years, has seriously threatened grain production and sustainability. The objective of this study is to evaluate water footprint, groundwater table, and system productivity through a three-year field experiment that focuses on transitioning from the conventional winter wheat-maize (WM) to winter wheat-soybean (WS) system, while integrating suitable irrigation strategies. Micro-sprinkling irrigation strategies were applied during the winter wheat season, when the soil water content (SWC) of the 40 cm soil layer dropped to 40% of its field capacity (FC). Specifically, W4 treatment irrigated until SWC reached 60% FC at a depth of 40 cm, while the W6 treatment irrigated to SWC reaching 80% FC at a 60 cm depth. In contrast, a rain-fed (W0) treatment served as the control. Field water consumption was simulated using the Water Heat Carbon Nitrogen Simulator (WHCNS) model. The results revealed that the WS system exhibited less variability in evapotranspiration (ETc) compared to WM system, with reductions ranging from 23.6% to 29.1%. Furthermore, the WS system contributed substantially to elevating the groundwater table by 58.4–146.4% while maintaining a higher and more stable annual wheat equivalent yield (WEY) compared to the WM system. The W4 treatment saved 97.9–98.2 mm of irrigation water compared to the W6 treatment, improved water productivity by 10.7–32.1%, and reduced the water footprint by 14.3–25.1%. Transitioning from the traditional WM cropping system to the WS system, and adapting an appropriate irrigation regime (W4) can counterbalance extreme weather impacts on crop yields. This study provides valuable insights into sustainable farming practices, and it may provide a practical framework for striking a balance between groundwater conservation and food security. [Display omitted] • Traditional farming practices declining groundwater, challenges for food production. • Winter wheat-soybean (WS) pattern increase system yield and water productivity. • WS pattern reduced water consumption and water footprint by 27.97% and 41.58%. • WS pattern with W4 irrigation gradient can relieve groundwater depletion. [ABSTRACT FROM AUTHOR]