Watershed nitrogen (N) budgets provide insights into drivers and solutions for groundwater and surface water N contamination. We constructed a comprehensive N budget for the transboundary Nooksack River Watershed (BC, Canada and WA, US) using locally-derived data, national statistics and standard parameters. Feed imports for dairy (mainly in the US) and poultry (mainly in Canada) accounted for 30 and 29% of the total N input to the watershed, respectively. Synthetic fertilizer was the next largest source contributing 21% of inputs. Food imports for humans and pets together accounted for 9% of total inputs, slightly lower than atmospheric deposition (10%). Returning salmon represented <0.06% of total N input but was an important ecological flux by importing marine-derived nutrients. Quantified N export was 80% of total N input, driven by ammonia emission (32% of exports). Animal product export was the second largest output of N (31%) as milk and cattle in the US and poultry products in Canada. Riverine export of N was estimated 28% of total N export. The commonly used crop nitrogen use efficiency (crop NUE) alone did not provide sufficient information on farming activities and should be combined with other criteria such as farm-gate NUE to understand management efficiency. Agriculture was the primary driver of N inputs to the environment despite widespread adoption of conservation practices, illustrating a need to optimize management to minimize hydrologic and volatilization losses. The N budget provides key information for stakeholders across sectors and borders to create environmentally and economically viable and effective solutions.