Nitrogen applied to the surface of the land for agricultural purposes represents a significant source of reactive nitrogen (N<sub>r</sub>) that can be emitted as a gaseous N<sub>r</sub> species, be denitrified to atmospheric nitrogen (N<sub>2</sub>), run off during rain events or form plant-useable nitrogen in the soil. To investigate the magnitude, temporal variability and spatial heterogeneity of nitrogen pathways on a global scale from sources of animal manure and synthetic fertilizer, we developed a mechanistic parameterization of these pathways within a global terrestrial land model, the Community Land Model (CLM). In this first model version the parameterization emphasizes an explicit climate-dependent approach while using highly simplified representations of agricultural practices, including manure management and fertilizer application. The climate-dependent approach explicitly simulates the relationship between meteorological variables and biogeochemical processes to calculate the volatilization of ammonia (NH<sub>3</sub>), nitrification and runoff of N<sub>r</sub> following manure or synthetic fertilizer application. For the year 2000, approximately 125 Tg N yr<sup>−1</sup> is applied as manure and 62 Tg N yr<sup>−1</sup> is applied as synthetic fertilizer. We estimate the resulting global NH<sub>3</sub> emissions are 21 Tg N yr<sup>−1</sup> from manure (17 % of manure production) and 12 Tg N yr<sup>−1</sup> from fertilizer (19 % of fertilizer application); reactive nitrogen runoff during rain events is calculated as 11 Tg N yr<sup>−1</sup> from manure and 5 Tg N yr<sup>−1</sup> from fertilizer. The remaining nitrogen from manure (93 Tg N yr<sup>−1</sup>) and synthetic fertilizer (45 Tg N yr<sup>−1</sup>) is captured by the canopy or transferred to the soil nitrogen pools. The parameterization was implemented in the CLM from 1850 to 2000 using a transient simulation which predicted that, even though absolute values of all nitrogen pathways are increasing with increased manure and synthetic fertilizer application, partitioning of nitrogen to NH<sub>3</sub> emissions from manure is increasing on a percentage basis, from 14 % of nitrogen applied in 1850 (3 Tg NH<sub>3</sub> yr<sup>−1</sup>) to 17 % of nitrogen applied in 2000 (21 Tg NH<sub>3</sub> yr<sup>−1</sup>). Under current manure and synthetic fertilizer application rates we find a global sensitivity of an additional 1 Tg NH<sub>3</sub> (approximately 3 % of manure and fertilizer) emitted per year per °C of warming. While the model confirms earlier estimates of nitrogen fluxes made in a range of studies, its key purpose is to provide a theoretical framework that can be employed within a biogeochemical model, that can explicitly respond to climate and that can evolve and improve with further observation.