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.

Watershed‐scale carbon budgets remain poorly understood, in part due to inadequate simulation tools to assess in‐stream carbon fate and transport. A new numerical model termed ISOtope‐based FLuvial Organic Carbon (ISOFLOC) is formulated to simulate the fluvial organic carbon budget in watersheds where hydrologic, sediment transport, and biogeochemical processes are coupled to control benthic and transported carbon composition and flux. One ISOFLOC innovation is the formulation of new stable carbon isotope model subroutines that include isotope fractionation processes in order to estimate carbon isotope source, fate, and transport. A second innovation is the coupling of transfers between carbon pools, including algal particulate organic carbon, fine particulate and dissolved organic carbon, and particulate and dissolved inorganic carbon, to simulate the carbon cycle in a comprehensive manner beyond that of existing watershed water quality models. ISOFLOC was tested and verified in a low‐gradient, agriculturally impacted stream. Results of a global sensitivity analysis suggested the isotope response variable had unique sensitivity to the coupled interaction between fluvial shear resistance of algal biomass and the concentration of dissolved inorganic carbon. Model calibration and validation suggested good agreement at event, seasonal, and annual timescales. Multiobjective uncertainty analysis suggested inclusion of the carbon stable isotope routine reduced uncertainty by 80% for algal particulate organic carbon flux estimates.