<p>Natural and human factors have significantly altered the nitrogen and phosphorus content in surface water. While existing research predominantly focuses on the impact of human activities on these changes within large ecological watersheds, there is a notable gap in understanding the effects of climate factors and air pollution on the ecological environment of watersheds. This paper aims to bridge this gap by employing various analytical methods to establish a backdrop of climatic conditions, including precipitation, temperature, and atmospheric pressure. It investigates the effects and underlying mechanisms of atmospheric pollutants such as PM2.5, PM10, NO₂, SO₂, and O₃, alongside surface vegetation growth patterns—measured by the normalized vegetation index and surface vegetation coverage—on the nitrogen and phosphorus concentrations in the Fengle River. Our findings indicate a significant, albeit weak, negative correlation between seasonal differences in total phosphorus and O₃, temperature, and rainfall (R² = −  0.45, − 0.38, − 0.39; <i>P</i> &lt; 0.05, statistically significant). Conversely, no significant correlation was observed between seasonal variations in total nitrogen and seasonal shifts in climate or atmospheric pollutants (<i>P</i> &gt; 0.05, non-significant). The results underscore that atmospheric pressure substantially influences nitrogen and phosphorus nutrients in the Fengle River by modulating O₃, normalized vegetation index, and surface vegetation coverage. temperature was found to significantly affect the nutrient content in the water body by influencing levels of PM2.5, NO₂, and O₃, while rainfall had a notable impact on nutrient concentrations through its effects on PM2.5, PM10, and NO₂.</p>