A large amount of nitrogen remains in ion-absorption rare earth tailings with in-situ leaching technology, and it continually ends up in groundwater sources. However, the distribution and transport of ammonium nitrogen (NH4+-N) and nitrate nitrogen (NO3−-N) across tailings with both depth and hill slopes is still unknown. In this study, the amount of NH4+-N and nitrate nitrogen (NO3−-N) was determined in tailings, and a soil column leaching experiment, served to assess the transport and distribution following mine closure. Firstly, a high concentration of NH4+-N in the leachate at the initial leaching stage was detected, up to 2000 mg L−1, and the concentration of NH4+-N clearly diminished as time passed. Meanwhile, the NH4+-N contents remained relatively high in soil. Secondly, both the content of NH4+-N and NO3−-N varied greatly according to vertical distribution after leaching lasting several years. The amounts of NH4+-N and NO3−-N in surface soil were much smaller than those in deep soil, with 3–4 orders of magnitude variation with depth. Thirdly, when disturbed by NH4+-N, the pH not only diminished but also changed irregularly as depth increased. Fourthly, although the amount of NO3−-N was smaller than that of NH4+-N, both their distribution trend was similar with depth. In fact, NH4+-N and NO3−-N were significantly correlated but this declined from the knap to the piedmont. Based on these results, it is suggested that mining activity could cause nitrogen to be dominated by NH4+-N and acidification in a tailing even if leaching occurs over several years. NO3−-N derived from NH4+-N transports easily and it becomes the main nitrogen pollutant with the potential to be a long-lasting threat to the environment around a mine.