<p>Nitrogen (N) losses driven by rapid hydrologic processes in karst regions were once considered a potentially key mechanism of N limitation during the initial phase of natural recovery following karst desertification. However, field data are still lacking for studying the hydrologic N budget. To address this issue, we monitored the rainfall and N-related hydrologic processes in karst grass and grass–shrub ecosystems for 3&#xa0;years. Our results showed rainfall N input of 12.0&#xa0;kg N ha⁻¹ y⁻¹, of which 56.1% was inorganic N. Hydrologic N loss was 8.1 and 9.0&#xa0;kg N ha⁻¹ y⁻¹ in karst grass and grass–shrub ecosystems, respectively, and both had no significant difference. The mean hydrologic N loss was 8.5&#xa0;kg N ha⁻¹ y⁻¹, of which 74.1% was dissolved organic N (DON). Rainfall net N gain was 3.9 and 3.0&#xa0;kg N ha⁻¹ y⁻¹ in karst grass and grass–shrub ecosystems, respectively, and both had no significant difference. The mean rainfall net N gain was 3.4&#xa0;kg N ha⁻¹ y⁻¹, and inorganic N contributed vastly to net N gain, while DON was a net loss. Most rainfall inorganic N was retained by the soil, while DON loss was mainly derived from soil, indicating N exchange between rainfall and soil during the hydrologic process. Our results also showed that 76% of rainfall occurred in the rainy season, while disproportionately contributing to 56.5% of hydrologic N loss, which resulted in higher net N gain in the rainy season compared with that in the dry season. We speculate that the three-layer vertical structure of soil–epikarst–bedrock in karst areas induce a complex hydrologic process, prolonging the time of water–soil interaction, and leading to a maximum threshold for hydrologic N losses under high rainfall, which effectively protect soil inorganic N. Thus, rainfall can be considered an important source of N supply in karst grass and grass–shrub ecosystems, which helps alleviate the N limitation in the early karst succession stage.</p>