DOC and nitrate in farmland represent key chemical species that determine the water quality in the Karst Critical Zone (KCZ). The work reported here focuses on quantifying fluxes of these species in an experimental farm site (University of Leeds Farm, UK) overlying a dolomitic karst aquifer of Permian age. In this research, the Transect Method was applied for the first time to farmland by combining hydrochemical data from soil and groundwater for computation of mass fluxes. The Transect Method, developed for management of industrially contaminated sites, was applied to a farm source due to the presence of localised contamination from application of pig slurry.Required inputs for our approach include concentrations of nitrate and DOC in soil water and groundwater, net recharge flux (here derived from a MODFLOW-2005 model) and local hydraulic gradient and conductivity measurements. Key outputs are fluxes and downstream groundwater concentrations of DOC and nitrate. Downstream concentrations were validated against direct groundwater measurements, demonstrating the veracity of the approach. The approach shows that the localised contamination has a significant impact on both concentrations of nitrate and DOC in groundwater, although the DOC impact is greater, because the upstream land uses also produce nitrate as a result of agricultural practices that are widespread in the region.The results of the study also constrain the zone vulnerable to contamination to the upper ∼40 m below the ground surface. Future modelling efforts on solute contaminant transport should focus on this shallow vulnerability zone (0–40 mBGL) and the Transect Method applied in this work can be used to define boundary conditions.Hence, following this research, we envisage to export a generic approach that combines physical flow parameters and hydrochemical analyses for computation of subsurface mass fluxes using the Transect Method, to identify the degree of impact of specific point sources and to support conceptualization and modelling of contaminant transport in the KCZ of farm areas.