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The Midwest state of Iowa in the US is one of the major producers of corn, soybean, ethanol, and animal products, and has long been known as a significant contributor of nitrogen loads to the Mississippi river basin, supplying the nutrient-rich water to the Gulf of Mexico. Nitrogen is the principal contributor to the formation of the hypoxic zone in the northern Gulf of Mexico with a significant detrimental environmental impact. Agriculture, animal agriculture, and ethanol production are deeply connected to Iowa’s economy. Thus, with increasing ethanol production, high yield agriculture practices, growing animal agriculture, and the related economy, there is a need to understand the interrelationship of Iowa’s food-energy-water system to alleviate its impact on the environment and economy through improved policy and decision making. In this work, the Iowa food-energy-water (IFEW) system model is proposed that describes its interrelationship. Further, a macro-scale nitrogen export model of the agriculture and animal agriculture systems is developed. Global sensitivity analysis of the nitrogen export model reveals that the commercial nitrogen-based fertilizer application rate for corn production and corn yield are the two most influential factors affecting the surplus nitrogen in the soil.