Objective In arid and semi-arid regions, the ecological functions of farmland shelterbelts are critically dependent on soil quality, which is profoundly shaped by irrigation water sources. In the Ulan Buh Desert area, characterized by high evapotranspiration and scarce precipitation, a trade-off is observed between using mineral-laden Yellow River water and using saline groundwater for irrigation. However, the long-term effects of these two water sources on the coupled dynamics of soil nutrients and salt content in shelterbelt systems remain unclear. This study aims to elucidate the regulatory mechanisms of different irrigation water sources on soil nutrient-salt content interactions, thereby providing guidance for sustainable irrigation management.

Methods A typical farmland shelterbelt system in Dengkou county, Inner Mongolia, was selected for this study. Two irrigation treatments were compared: long-term Yellow River water irrigation and long-term groundwater irrigation, each with six replicate plots. Soil samples were collected in July (two weeks after the final irrigation) from five soil depth layers (0–100 cm, at 20 cm intervals). Eight soil nutrient indicators (e.g., organic matter, total nitrogen, ammonium nitrogen, nitrate nitrogen, available phosphorus, and available potassium) and nine salt ions (e.g., Na⁺, Cl⁻, and SO₄²⁻) were measured. Data were analyzed using one-way ANOVA and correlation analysis.

Results Compared with groundwater irrigation, Yellow River water irrigation significantly increased the mean contents of soil organic matter (6.85 vs. 3.41 g/kg), total nitrogen (0.45 vs. 0.27 g/kg), ammonium nitrogen (10.39 vs. 8.78 mg/kg), and available potassium (282.11 vs. 234.97 mg/kg) in the 0–100 cm soil layer. Higher spatial stability of these nutrients (coefficient of variation, CV: 4.07%–21.64%) was also observed under Yellow River irrigation. However, under Yellow River irrigation, nitrate nitrogen showed significant leaching in the 40–60 cm layer (P < 0.05). Conversely, groundwater irrigation led to surface accumulation of nitrate nitrogen (4.27 mg/kg) and available phosphorus (13.24 mg/kg). Critically, the mean total salt content under groundwater irrigation was three times that under Yellow River irrigation. In the 80–100 cm layer, Cl⁻ and Na⁺ concentrations under groundwater irrigation were 23.8 times and 8.23 times higher, respectively, than those under Yellow River irrigation. Correlation analysis revealed that, under Yellow River irrigation, organic matter was negatively correlated with salt ions (e.g., Na⁺, Cl⁻), whereas a synergistic accumulation of nutrients and salts was observed under groundwater irrigation.

Conclusions Long-term irrigation with Yellow River water is more effective in maintaining surface soil nutrients and preventing salt accumulation, thereby resulting in a lower risk of soil salinization. Although groundwater irrigation provides short-term benefits for certain nutrients, it induces a high risk of severe salt accumulation in deep soil layers, particularly Cl⁻ and Na⁺. Therefore, groundwater irrigation should be complemented with drainage systems or mixed with Yellow River water to balance nutrient supply and salt hazard control. The objectives of this study are achieved, as the differential mechanisms of the two water sources on soil nutrient and salt dynamics are clearly identified.