A detailed fixed nitrogen (N) mass balance was constructed for the Central Arizona–Phoenix (CAP) ecosystem. Input of fixed N input to the ecosystem was 98 Gg y−1. Of this, humans deliberately imported or mediated the fixation of 51 Gg N y−1; combustion processes added another 36 Gg y−1. Fixation by desert plants, wet deposition, and surface water input accounted for 11% of total N input. Total fixed N output was 78 Gg N y−1, a large component of which was gaseous N products of combustion and denitrification. Computed accumulation of N was 21 Gg y−1 (total input minus total output) or alternatively, 17 Gg y−1 (summing individual accumulation fluxes). Key uncertainties include dry deposition of atmospheric N and changes in soil storage. Inputs to the urban and agricultural components of the ecosystem were an order of magnitude higher than inputs to the desert. Human hydrologic modifications in this ecosystem promote the accumulation and volatilization of N while keeping riverine export low (3% of input). Interplay among the form and amount of N inputs, edaphic and climatic characteristics of the system, hydrologic modifications, and deliberate efforts to reduce N pollution controls the fate of N in human-dominated ecosystems.