Ammonium sulfate is widely used as leaching agent for the in-situ leaching mining of ionic rare earth. The residual leaching chemicals such as ammonia nitrogen might migrate along with the catchment process, causing serious pollution of soil and water environment in mining area. In order to reveal the surface migration characteristics of ammonia nitrogen pollution at the basin scale, field sampling was conducted in a small basin of an ionic rare earth mining area in southern Jiangxi during the rainy season when the catchments were most intense. The surface migration and distribution characteristics of ammonia nitrogen and nitrate nitrogen in the mining basin were studied by means of GIS hydrological analysis and other means. The results showed that the contents of leaching agent in the channel sediment and surface soils were sorted as:channel deposits > collapsed hillslope > natural hillslope. The content of residual leaching agent in the channel deposits was positively correlated with the finer particle composition. On average, the ammonia nitrogen concentration in the main channel of the watershed was measured as 95.12 mg/L with the outlet value of 115 mg/L, which has exceeded the standard by 6.7 times. For some branch gullies in the mining area, the ammonia nitrogen could exceed the standard by as high as 24.5 times. A typical branch gully illustrated an exponential increasing leaching agent concentration in runoff with the accumulative flow area. On the other hand, the runoff leaching agent concentration in the main channel showed a fluctuation trend composed by sudden increase and steady attenuation. An estimation model of ammonia nitrogen concentration along the main channel was established by comprehensively considering the inflow of both the contaminated and natural water, and it was proved to be reliable by the model efficiency of 0.79. The above results preliminarily clarified the migration and distribution of the residual leaching agent in the small watershed of ionic rare earth mining area in rainy seasons, and in turn it could be helpful for evaluating water and soil pollution risk in the watershed and guiding the ecological restoration measurements.