Planting rice is a beneficial strategy for improving soda saline-alkali soil, but it comes with the challenge of increased runoff discharge of salt and fluoride (F−) ions. The use of different nitrogen (N) fertilizers can impact this ion discharge, yet the specific characteristics of ion runoff under different N-fertilizer applications remain unclear. A field experiment was conducted in this study, applying five commonly used N-fertilizer types to monitor the ion runoff throughout an entire rice growing season. Salt ions and F− runoff discharge was significantly affected by N-fertilizer type, runoff event, and their interaction (p < 0.001). Regardless of N-fertilizer types, sodium (Na+) and bicarbonate (HCO3−) ions were consistently discharged from runoff in soda saline-alkali fields, constituting 20.55–25.06 % and 47.57–50.49 % of total ion discharges, respectively. Compared to no N-fertilizer (CK) and other N-fertilizer treatments, the organic-inorganic compound fertilizer (OCF) application significantly reduced Na+ and HCO3− runoff discharge, causing a decrease in the competitive adsorption capacity between HCO3− and F− (p < 0.05). The use of OCF and inorganic compound fertilizer (ICF) lowered pH in runoff water, resulting in reduced dissolution capacity of calcium fluoride in the soil and thereby decreasing total F− runoff discharge. In conclusion, OCF proves to be an effective N-fertilizer in mitigating salt ions and F− runoff discharge in soda saline-alkali paddy fields. Additionally, ICF demonstrates the ability to control F− runoff discharge.