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The characteristics of nitrate vertical transport in soils collected from Libo and Puding in Guizhou Province were studied by simulating soil column in laboratory. The results were as follows: (1) Vertical transport velocity of nitrate decreased, and the breakthrough curves (BTCs) of nitrate were more dispersed, in each horizon from surface layer to bottom layer in every soil profile. As rocky desertification progressed, the BTCs experienced a gentle up and down trend, and tailing was more obvious. (2) An analytical solute transport model (CXTFIT 2.0) was used to estimate nitrate dispersion coefficient (D) and average pore water velocity (V) from the observed BTCs. The results showed that CXTFIT 2.0 model was suitable in fitting the nitrate transport in these soils. The dispersion coefficient was found to be a function of average pore water velocity. (3) The transport of nitrate was mainly affected by the soil structural coefficient. As soil structural coefficient decreased, nitrate outflow was retarded, and the peak concentration was reduced. Soil bulk density, organic matter, and clay also affected the vertical transport of nitrate. Low bulk density, clay content, and high organic matter content were each associated with faster nitrate transport.