In Groundwater-Dependent Terrestrial Ecosystems (GWDTEs), atmospheric nitrogen (N) inputs have often been studied in isolation from terrestrial groundwater and surface water inputs. We describe for the first time the development and application of a combined atmospheric and terrestrial N source apportionment methodology, able to identify contributing catchment and N loadings to GWDTEs. We combined all N inputs using a site-specific conceptual model supported by 12 months’ monitoring for a Chalk-fed GWDTE at Newbald Becksies, East Yorkshire. We discuss implications for effective catchment management, wetland protection and development of a source apportionment methodology. Potential sources of nitrate include: atmospheric deposition, mineralization, leaching from agricultural soils, manure heaps, septic tanks, sewer and mains water leakage. Atmospheric deposition was calculated from measurements of ammonia and nitrogen dioxide concentrations together with rainfall inputs of ammonium and nitrate. Quantification of agricultural sources used the FarmScoper modelling tool to estimate nitrate leaching in the groundwater catchment. Comparison between modelled nitrate concentrations in leachate (15–17 mg N l⁻¹) and observed groundwater nitrate concentrations (12.3–19.8 mg N l⁻¹) are good. The majority of nitrate is leached from arable land. FarmScoper allows mitigation scenarios to be tested, supporting measures to reduce nitrate within a groundwater catchment.