Although numerous studies on nitrate transport and transformation in karst catchments have been reported, many challenges in understanding nitrate fluxes remain due to the unique architecture of karst critical zones and complex hydrological processes. Water age is an important descriptor of hydrological function providing insight to into flow paths and water sources at the catchment scale. This offers a potential opportunity to better understand the spatio-temporal variations in nitrate dynamics in karst catchments. We linked the nitrate dynamics of underground conduit flow to water age extracted from a robust tracer-aided model for a karst catchment in southwestern China. The results show that nitrate dynamics in underground conduit flow are controlled by the coupling of nitrate supply and of flow paths in the karst catchment. High contributions of drainage from small fractures water leads to low nitrate concentrations in underground conduit flow during the dry season. This reveals that the small fractures may be another important "hot spot" for denitrification leading to nitrate removal in the karst critical zone. The switching between transport limited and supply limited conditions cause the marked variations in nitrate concentration of underground conduit flow during wet season. Although rapid infiltration via large fractures and sinkholes have strong dilution effects on nitrate in underground conduit flow at beginning of rainfall, more nitrate was transported out of the catchment with drainage during rainfall events due to the mobilization of soil nitrate by rainfall. Meanwhile, the capacity to transport nitrate out of catchment can be potentially activated when the `old' water is displaced by rainfall under high wetness condition.