Agricultural land in karst systems can pollute water courses, with polluted waters travelling quickly to and through the sub-surface. Understanding how rapidly nitrate moves within the highly-transmissive karst critical zone (from soils to aquifers) is limited by low resolution data. To understand nitrate behavior and its controls, we deployed sensor technology at five sites to generate autonomously high-resolution time series of discharge and NO₃⁻–N, which is the major nitrogenous component, in a farmed karst catchment in Southwestern China. The [NO₃⁻–N] time series exhibited rapid response to rainfall-induced increases in discharge and a large magnitude in [NO₃⁻–N], from 0.72 to 16.3 mg/L across five sites. However, the magnitude of NO₃⁻–N response at each site was varied during rainfall events (wet season) and dry season. The highest mean [NO₃⁻–N] and normalized annual fluvial export occurred in a headwater catchment with a developed karst aquifer system. Seasonal variation in NO₃⁻–N export occurred in response to source availability, most notable in catchments with valley agriculture: in the wet season up to 94% of nitrate was exported from the headwater catchments within two months, but at the larger catchment scale, over the 6 month wet season, only 61% of total export occurred. At the larger catchment scale, [NO₃⁻–N] were lower due to buffering by the karstic aquifer network. From the time series we observe little decrease in [NO₃⁻–N] as discharge decreases in the dry season, indicating the karst aquifers are chronically-polluted with nitrate through slow flow pathways.