Nitrogen (N) contamination within agricultural‐karst landscapes and aquifers is widely reported; however, the complex hydrological pathways of karst make N fate difficult to ascertain. We developed a hydrologic and N numerical model for agricultural‐karst, including simulation of soil, epikarst, phreatic, and quick flow pathways as well as biochemical processes such as nitrification, mineralization, and denitrification. We tested the model on four years of nitrate (NO₃⁻) data collected from a phreatic conduit and an overlying surface channel in the Cane Run watershed, Kentucky, USA. Model results indicate that slow to moderate flow pathways (phreatic and epikarst) dominate the N load and account for nearly 90% of downstream NO₃⁻ delivery. Further, quick flow pathways dilute NO₃⁻ concentrations relative to background aquifer levels. Net denitrification distributed across soil, epikarst, and phreatic water removes approximately 36% of the N inputs to the system at rates comparable to nonkarst systems. Evidence is provided by numerical modeling that NO₃⁻ accumulation via evapotranspiration in the soil followed by leaching through the epikarst acts as a control on spring NO₃⁻ concentration and loading. Compared to a fluvial‐dominated immature karst system, mature‐karst systems behave as natural detention basins for NO₃⁻, temporarily delaying NO₃⁻ delivery to downstream waters and maintaining elevated NO₃⁻ concentrations for days to weeks after hydrologic activity ends. This study shows the efficacy of numerical modeling to elucidate complex pathways, processes, and timing of N in karst systems.