© 2019 Elsevier B.V. Excessive nutrient loading from small agricultural headwaters can substantially degrade downstream water quality and ecological conditions. But, our understanding of the scales and locations to implement nutrient attenuation tools within these catchments is poor. To help inform farm- and catchment-scale management, we quantified nitrate export in nine one-kilometre-long lowland agricultural headwaters fed by tile and open tributary drains in a region with high groundwater nitrate (<1 to >15 mg L −1 NO 3 -N) over four years. Across-catchment differences in upstream spring water nitrate concentrations predicted differences in annual nitrate loads at catchment outlets (range <1–72 megagrams NO 3 -N 365 d −1 ), and nitrate loads were higher in wet seasons and wet years, reflecting strong groundwater influences. Partitioning the sources of variability in catchment nitrate fluxes revealed that ~60% of variation was accounted for by a combination of fluxes from up-stream springs and contributions from tile and open tributary drains (46% and 15%, respectively), with ~40% of unexplained residual variation likely due to groundwater upwellings. Although tile and open tributary drains contributed comparatively less to catchment loads (tile drains: <0.01 and up to 50 kg NO 3 -N d −1 ; open drains: <5 kg and up to 100 kg NO 3 -N d −1 ), mitigation targeted at these localised, farm-scale sources will contribute to decreasing downstream nitrate fluxes. However, high nitrate loads from groundwater mean current NO 3 -N waterway management and rehabilitation practices targeting waterway stock exclusion by fencing alone will be insufficient to reduce annual NO 3 -N export. Moreover, managing catchment nutrient fluxes will need to acknowledge contributions from groundwater as well as farm-scale losses from land. Overall, our results highlight how nutrient fluxes in spring-fed waterways can be highly dynamic, dominated more by groundwater than local run-off, and point to the scales and locations where nitrate attenuation tools should be implemented.