With global climate change, flooding events are becoming more frequent. However, the mechanism of how waterlogging stress affects crop roots needs to be studied in depth. Waterlogging stress can also lead to soil nitrogen and phosphorus loss, resulting in agricultural surface pollution. The aim of this study is to clarify the relationship between soil nitrogen and phosphorus distribution, root growth characteristics, and nitrogen and phosphorus loss in runoff water under waterlogging stress during the winter wheat seedling stage. In this paper, Zhengmai 136 was selected as the experimental material, and two water management methods (waterlogging treatment and non-waterlogging control treatment) were set up. Field experiments were conducted at the Wudaogou Hydrological Experimental Station in 2022 to assess the nitrogen and phosphorus concentrations in runoff water under waterlogging stress. The study also aimed to analyze the nitrogen and phosphorus content and the root distribution characteristics in different soil layers under waterlogging stress. The results showed as the following: 1. Waterlogging stress increased the characteristic parameters of winter wheat roots in both horizontal and vertical directions. Compared with the control treatment, the root length increased by 1.2–29.9% in the waterlogging treatment, while the root surface area and volume increased by an average of 3.1% and 41.9%, respectively. 2. Nitrogen and phosphorus contents in waterlogged soils were enriched in the 0–20 cm soil layer, but both tended to decrease in the 20–60 cm soil layer. Additionally, there was an inverse relationship between the distribution of soil nutrients and the distribution of wheat roots. 3. During the seedling stage of winter wheat, nitrogen loss was the main factor in the runoff water. In addition, nitrate nitrogen concentration averaged 55.2% of the total nitrogen concentration, while soluble phosphorus concentration averaged 79.1% of the total phosphorus concentration. 4. The results of redundancy analysis demonstrated that available phosphorus in the soil was the key environmental factor affecting the water quality of runoff water. Total phosphorus and dissolved phosphorus in the water were identified as the dominant factors influencing root growth.
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