Display omitted •Use HYDRUS to simulate transport of in-situ leaching agent in a hilly rare earth mine.•Spatiotemporal distribution of soil NH4-N and NO3-N is highly heterogeneous across the hill.•Five years of rainwater leaching could remove <10% of soil NH4-N from the hill.•Nitrification and lateral flow led to buildup of NO3-N near surface at the bottom of the hill. The large amount of residual soil ammonium nitrogen (NH4-N) after in-situ leaching is a legacy environmental issue for ionic rare earth mines. Understanding and mitigating the associated risk to the aquatic ecosystems of the mining as well as its downstream areas would benefit from a quantitative description and prediction of NH4-N transformation and transport during and after in-situ leaching. Up to date, studies related to the transport and leaching characteristics of residual soil NH4-N have been mostly limited to laboratory experiments. Few field process-based studies of the transport behaviors of residual leaching agents in rare earth mines have been conducted partially because of their remote locations, restricted accessibility, and scarce background data. Based on field investigations at a remote hilly rare earth mine in Ganzhou City, Southern China, we established a HYDRUS-2D model to simulate the transport and transformation of soil NH4-N in the mine throughout in-situ leaching, flushing, and subsequent rainwater leaching. Though subjected to conceptual generalization and limited background data, the established HYDRUS-2D model was able to satisfactorily simulate the observed distinctively different vertical soil NH4-N and nitrate nitrogen (NO3-N) profiles at the top, middle, and bottom of the hill in March 2021, with R2 ranging from 0.71 to 0.89 for soil NH4-N and 0.69 to 0.86 for soil NO3-N. Further analysis of the HYDRUS simulation results revealed a much different spatiotemporal distribution pattern between soil NH4-N and NO3-N throughout the simulation period. For soil NH4-N, the shape and spatial extent of its distribution was largely determined by in-situ leaching, whereas flushing and rainwater leaching slowly pushed its spatial extent further downward, and to a less extent downslope to the right. Flushing and five years of rainwater leaching could merely remove around 10% of residual soil NH4-N from the hill. Unlike NH4-N, the spatial distribution pattern of soil NO3-N varied considerably among various phases of in-situ leaching, flushing, and rainwater leaching. Soil water movement affected the spatial distribution of soil NO3-N considerably, which was especially evident from its significant buildup near surface at the bottom of the hill. Overall, our study results have revealed the critical role of continuous water movement and solute transport in shaping the distribution patterns of residual leaching agents in rare earth mining regions. The proposed HYDRUS model may serve as a promising framework for investigating the transport and spatiotemporal distribution of in-situ leaching agent in rare earth mining regions with scarce background data. It also has great potentials in facilitating the development of more effective in-situ leaching programs and the design of suitable water pollution control and ecological remediation measures.