In order to reveal the effects of rainfall on nitrogen export and the characteristics of nitrogen export in a Karst small catchment, this paper studied a typical small agricultural catchment in the Karst area, i.e. Houzhai catchment in Guizhou Province. This study monitored and tested concentrations of various forms of nitrogen in samples from sinkhole, surface water, and groundwater to estimate the annual flux of nitrogen during the rainy season, and investigated the effects of rainfall on nitrogen export with regional precipitation data. The results indicated that: (1) Nitrogen concentration in the Houzhai catchment was considerably higher than those in the large rivers in China: The average concentration of TDN was 6.5 mg/L in the groundwater system and 7.3 mg/L in the surface water system. (2) The main nitrogen form was NO3--N, with a small amount of NH4+-N, NO2--N, and DON export in the Houzhai small catchment. (3) The estimated flux of the TDN, NO3--N, NH4+-N, NO2—N, and DON output was 55.13, 52.12, 0.40, 0.01, and 2.61 t, respectively, in the Houzhai catchment during the rainy season. (4) The continuous precipitation over a couple of days accelerated nitrogen loss in the Karst area. The NO3--N concentration in the upstream increased after the beginning of rainfall events and decreased after the termination of precipitation. Moreover, there was an observable hysteresis between the change in NO3--N concentration with the occurrence of rainfall at the outlet of the catchment.