The waterway network ship traffic, energy, and environment model (STEEM) is applied to geographically characterize energy use and emissions for interport ship movement for North America, including the United States, Canada, and Mexico. STEEM advances existing approaches by (i) estimating emissions for large regions on the basis of nearly complete data describing historical ship movements, attributes, and operating profiles of individual ships, (ii) solving distances on an empirical waterway network for each pair of ports considering ship draft and width constraints, and (iii) allocating emissions on the basis of the most probable routes. We estimate that the 172 000 ship voyages to and from North American ports in 2002 consumed about 47 million metric tonnes of heavy fuel oil and emitted about 2.4 million metric tonnes of SO2. Comparison with port and regional studies shows good agreement in total estimates and better spatial precision than current top-down methods. In quantifying limitations of top-down approaches that assume existing proxies for ship traffic density are spatially representative across larger domains, we find that International Comprehensive Ocean-Atmosphere Data Set (ICOADS) proxy data are spatially biased, especially at small scales. Emissions estimated by STEEM for ships within 200 nautical miles of the coastal areas of the United States are about 5 times the emissions estimated in previous studies using cargo as a proxy.