[Objective] Citrus production is one of the main income of farmers in the Three Gorges Reservoir area. The loss of nitrogen and phosphorus caused by excessive fertilizer in the Three Gorges Reservoir area present negative impacts on the aquatic environment.[Methods] In this study, sandy soil citrus orchard with natural grass mulching was chosen. The amount of nitrogen and phosphorus loss from surface runoff and leaching was observed for two consecutive years by plot experiment at six levels of fertilization. The pathways of nitrogen and phosphorus losses in the citrus orchard and the effects of different fertilization levels on nitrogen and phosphorus losses were investigated. Seven treatments were set in the experimental plot, with an average row and plant spacing of 4.7 m × 3.4 m; with no fertilizer application (T1) as the control, the application rates of nitrogen, phosphorus and potassium fertilizer for the T3, T4, T5, T6 and T7 treatments were 1.67, 2.33, 3.00, 3.67 and 4.33 times those of T2, respectively. During the growth season of navel orange in 2016—2017, rainfall and atmospheric deposition of nitrogen and phosphorus were monitored. Surface runoff water, sediment, and infiltration water were sampled for total nitrogen (TN) and total phosphorus (TP) content.[Results] Under the ecological protection mode of grass mulching, the surface runoff and soil erosion were effectively controlled. The main pathway of water loss in the rain-fed citrus orchard was leaching with a low coefficient of surface runoff and weak soil erosion. During the study period, the rainfall loss by seepage accounted for 48.9% of the rainfall, and the surface runoff only accounted for 1.73% of the rainfall. The amount of fertilization applied in deep furrow had no effect on the amount of nitrogen and phosphorus loss from the surface runoff. Leaching was the main pathway of nitrogen and phosphorus loss. The average leaching loss of total nitrogen and total phosphorus accounted for 99.0% and 76.9% of the total loss of nitrogen and total phosphorus respectively. Also, the amount of nitrogen loss (y) by seepage increased with the increase of application rates (x), and there was a significant linear correlation between them (y =0.35x–5.77, P<0.01). However, no significant correlation existed between the amount of phosphorus loss and application rates (P =0.05). Also, only a small amount of phosphorus can be leached to the bottom of the soil after the roots uptake and soil particles adsorption in up layers. Moreover, the residual phosphorus in the deep soil; after deep plough before citrus planting, had an impact on the leakage of phosphorus.[Conclusion] The problem of nutrient loss; leaching nitrogen loss in citrus orchards, in particular, should be given more attention. To reduce nutrient loss and achieve efficient utilization, nutrient management should be further optimized.