Transportation fuels flow through a complex supply chain from the point of crude oil extraction to the point of combustion. We present a model that tracks the movement of gasoline and diesel across the petroleum infrastructure network consisting of pipeline, tankers, trucks, trains, refineries, and blenders. While direct CO2 emissions, from combustion, outweigh all supply chain emissions from processing and fuel movement, the indirect CO2 emissions also contribute a not insignificant amount of emissions driven by demand of transportation fuels. We resolve county-scale supply chain (Scope 3) CO2 emissions using publicly accessible data to quantify fuel movement between different linkages and transportation modes across the country. For most of the US, the exact volume of fuel moved between counties, from different refineries, along different modes of transportation, is not explicitly known. Linear optimization is used to model these flows with supply and demand related constraints. This work presents the most complete view of spatially-resolved scope-3 style CO2 emissions from United States’ road transportation fuels. It offers a chance to investigate spatial patterns of scope-3 emissions across the country, as well as spatial differences between scope-1 and scope-3. Understanding embodied CO2 emissions of commodity flows across the US has implications for national and local policy.