The efficient provision of food, energy, and water (FEW) resources to cities is challenging around the world. Because of the complex interdependence of urban FEW systems, changing components of one system may lead to ripple effects on other systems. However, the inputs, intersectoral flows, stocks, and outputs of these FEW resources from the perspective of an integrated urban FEW system have not been synthetically characterized. Therefore, a standardized and specific accounting method to describe this system is needed to sustainably manage these FEW resources. Using the Detroit Metropolitan Area (DMA) as a case, this study developed such an accounting method by using material and energy flow analysis to quantify this urban FEW nexus. Our results help identify key processes for improving FEW resource efficiencies of the DMA. These include (1) optimizing the dietary habits of households to improve phosphorus use efficiency, (2) improving effluent-disposal standards for nitrogen removal to reduce nitrogen emission levels, (3) promoting adequate fertilization, and (4) enhancing the maintenance of wastewater collection pipelines. With respect to water use, better efficiency of thermoelectric power plants can help reduce water withdrawals. The method used in this study lays the ground for future urban FEW analyses and modeling.