The Lake Clearwater catchment, in the Canterbury high country of New Zealand, has a native ecosystem that is adapted to low nutrient conditions. Wetlands in the catchment are identified by the Department of Conservation’s Arawai Kākāriki Wetland Restoration Programme as one of three important endemic wetland types in New Zealand. Uncertainty regarding diffuse nutrient load from agriculture into the lake and wetland ecosystems is limiting effective management of the catchment. This study investigated hydrological processes and nitrogen and phosphorus concentrations to improve knowledge of the sources, characteristics and magnitude of nutrient loading from agricultural land use in this 46 km2 high country catchment. Relevant hydrological data and literature pertaining to the catchment was extensively reviewed. In addition, flow for five key surface waterways was continuously logged at ten sites for 2 years. Concurrently, nutrient concentrations for total nitrogen, nitrate, ammoniacal nitrogen, total phosphorus and dissolved reactive phosphorus were measured at ten surface water sites and three groundwater sites. Total nitrogen and phosphorus load from farmland was calculated from annual flow and median concentrations for four waterways: farmland perennial stream runoff, farmland ephemeral stream runoff, a wetland channel below the farmed hillslope and the lake outlet. Similarly, total nitrogen and phosphorus load for unfarmed land was calculated from the flow and median concentration of two un-impacted perennial streams. Total nitrogen and phosphorus mass balances were calculated and used to estimate subsurface nutrient load and runoff volume from the farmed hillslope. Estimates of subsurface runoff were also made using Darcy’s equation and a water balance. Nutrient load predictions from the Catchment Land Use for Environmental Sustainability (CLUES) model were compared to measured loads. Nutrients were found to be elevated downstream of farmland, especially nitrogen, which was often above relevant guidelines and typical concentrations in upland waterways in Canterbury. Nitrate in farmland subsurface runoff was elevated and was estimated to contribute 52% of total nitrogen yield from farmland. Total nitrogen yield (1.96-2.94 kg ha-1 year-1) for farmed land was comparable to minimum values for pastoral land use in literature but total phosphorus yield (0.093-0.123 kg ha-1 year-1) was well below published values. The range in yield estimates is due to subtraction of a high and a low estimate of natural baseline yield from the measured in-stream yield. Total nitrogen export from the lake (2518 kg year-1) was greater than estimated input (1375 kg year-1) from farmed and non-farmed land indicating an additional source of nitrogen into Lake Clearwater. Total phosphorus export from Lake Clearwater of 58 kg year-1 was 24% less than total estimated loads into the lake (76 kg year-1) from farmed and non-farmed land. Phosphorus was not often above relevant guidelines and the median total nitrogen to total phosphorus ratio in Lake Clearwater (49:1) indicated phosphorus is the limiting nutrient in the lake. Because phosphorus was less elevated relative to nitrogen, an increase in phosphorus inputs could have a greater effect on productivity in the wetland and lake. With corrected land use information, total nitrogen loads predicted by the CLUES model were reasonable but total phosphorus loads were greatly overestimated. Investigation into potential impacts of the elevated nutrient loads described in this study on receiving native ecosystems is recommended to inform conservation efforts.