In the Chesapeake Bay Watershed, excess nitrogen has contributed to poor water quality, leading to nitrogen mitigation efforts to restore and protect the watershed. The food production system is a top contributor to this nitrogen pollution. While the food trade plays a vital role in distancing the environmental impacts of nitrogen use from the consumer, previous work on nitrogen pollution and management in the Bay is yet to carefully consider the effect of embedded nitrogen found in products (nitrogen mass within the product) imported and exported throughout the Bay. Our work advances understanding across this area by creating a mass flow model of nitrogen embedded in the food production chain throughout the Chesapeake Bay Watershed that separates phases of the production and consumption processes for crops, live animals, and animal products and considers commodity trade at each phase by combining aspects of both nitrogen footprint and nitrogen budget models. Also, by tracking nitrogen embedded in products imported and exported in these processes, we distinguished between direct nitrogen pollution and nitrogen pollution externalities (displaced N pollution from other regions) from outside of the Bay. We developed the model for the watershed and all its counties for major agricultural commodities and food products for 4 years 2002, 2007, 2012, and 2017 with a specific focus on 2012. Using the developed model, we determined the spatiotemporal drivers of nitrogen loss to the environment from the food chain within the watershed. Recent literature leveraging mass balance approaches has suggested that previous long-term declines in nitrogen surplus and improvements in nutrient use efficiency have stagnated or begun to reverse. Our results suggest that within the Chesapeake Bay, increased corn and wheat acreage and steadily increasing livestock/poultry production may have led to the stagnation in decreasing N loss trends from agricultural production observed over the past two decades. We also show that at the watershed scale, trade has reduced the food chain nitrogen loss by about 40 million metric tons. This model has the potential to quantify the effect of various decision scenarios, including trade, dietary choices, production patterns, and agricultural practices, on the food production chain nitrogen loss at multiple scales. In addition, the model's ability to distinguish between nitrogen loss from local and nonlocal (due to trade) sources makes it a potential tool to optimize regional domestic production and trade to meet local watershed's needs while minimizing the resulting nitrogen loss.