Abstract. Nutrient contamination of surface and groundwaters is an issue of growing importance as the risks associated with agricultural runoff escalate due to increasing demands on global food production. In this study, the nutrient flux occurring within the surface and groundwaters of a lowland karst catchment in western Ireland was investigated with the aid of alkalinity sampling and a hydrological model. Water samples were collected and tested from a variety of rivers, lakes (or turloughs), boreholes and springs at monthly intervals over a three year period. Alkalinity sampling was used to elucidate the contrasting hydrological functioning between different turloughs. Such disparate hydrological functioning was further investigated with the aid of a hydrological model which allowed for an estimate of allogenic and autogenic derived nutrient loading into the karst system. The model also allowed for an investigation of mixing within the turloughs, comparing observed behaviours with the hypothetical conservative behaviour allowed for by the model. Results indicated that at the system outlet to the sea, autogenic recharge had added approximately 35% to the total flow and approximately 85% to the total N-load. Within some turloughs, nutrient loads were found to reduce over the flooded period, even though the turloughs hydrological functioning (and the hydrological model) suggested this should not occur. As such, it was determined that nutrient loss processes were occurring within the system. Denitrification was deemed to be the main process reducing nitrogen concentrations within the turloughs whereas phosphorus loss is thought to occur mostly within the diffuse/epikarst zone.