In a karst groundwater system, it develops complex multiple flows because of its special geological structure and unique physical patterns of aquifers. In order to investigate the characteristics and transport patterns of ammonia, nitrite and nitrate in epikarst water and subterranean stream, the water samples were collected monthly in a fast-urbanizing karst region. The results showed distinctive characteristics of three forms of inorganic nitrogen. The concentration of inorganic nitrogen was stable in the epikarst water while it was fluctuant in the subterranean stream. Epikarst water was less affected by rainfall and sewage compared with subterranean stream. In epikarst water, the nitrate concentration was much higher than the ammonia concentration. Dissolved inorganic nitrogen, mainly from non-point source pollution related to agricultural activities, passed in and out of the epikarst water based on a series of physical; chemical and biological processes in the epikarst zone, such as ammonification, adsorption and nitrification. On the contrary, subterranean stream showed a result of NH₄⁺-N > NO₃⁻-N in dry seasons and NO₃⁻-N > NH₄⁺-N in rainy seasons. This can be due to the fact that sanitary and industrial sewage flowed into subterranean river through sinkholes, fissures and grikes in dry season. Dissolved inorganic nitrogen in subterranean river was mainly from the non-point source pollution in wet season. Non-point source pollutants entered into subterranean water by two transport ways, one by penetration along with vadose flow through fissures and grikes, and the other by conduit flow through sinkholes from the surface runoff, soil water flow and epikarst flow. The export flux of DIN was 56.05 kg · (hm² · a)⁻¹, and NH₄⁺-N and NO₃⁻-N accounted for 46.03% and 52.51%, respectively. The contributions of point-source pollution and non point-source pollution to the export flux of DIN were 25.08% and 74.92%, respectively, based on run-off division method.