The Hetao Irrigation District (HID), a key agricultural base in China, faces severe non-point source nitrogen (N) and phosphorus (P) pollution due to intensive farming. Although nutrient stoichiometry governs C, N, and P cycling, decadal-scale comparisons and seasonal variations of these ratios in both soil and drainage water have yet to be fully elucidated. We examined total carbon (TC), total nitrogen (TN), total phosphorus (TP) and their ratios (C:N, C:P, N:P) in the HID soils and drainage water during 2012–2013 and 2021–2022. Soils under sunflower (SF), maize and other cash crops (MC) exhibited higher nutrient contents than uncultivated soils. Compared with 2012, MC showed higher TN but lower TP concentrations in 2021–2022. Seasonally, autumn soils generally exhibited higher TC and TN concentrations relative to TP, whereas TP concentrations were higher in summer. Drainage water in 2021–2022 was characterized by lower TC, TN, TP, and C:N ratios than in 2012–2013 across all irrigation districts. Seasonally, TC and TN concentrations were generally higher during spring and summer, whereas TP concentrations were higher in autumn. High C:P and N:P ratios were associated with relatively low P availability in the HID. Fertilization was strongly associated with soil nutrient concentrations, whereas irrigation district and climatic conditions were the primary factors associated with variation in stoichiometric ratios. Furthermore, soil TN exerted a direct influence on drainage water TN, while mean annual precipitation and temperature showed significant indirect and direct associations with drainage water nutrient concentrations, respectively. Consequently, regulating N application rates is imperative for mitigating eutrophication within the HID. This study establishes a robust data foundation for soil and drainage water management and provides a reliable scientific basis for controlling agricultural non-point source pollution in the region.