Shipping in the Great Lakes-St. Lawrence River Maritime Transportation System (MTS) is a more energy efficient transportation mode than road or rail transportation, thanks to the large capacity of vessels and the relatively low friction associated with moving a vessel through water. As a result, marine shipping emits the lowest amount of carbon per ton-mile, relative to road or rail transportation. A 2011 study by the Research and Traffic Group found that, on a ton-per-mile basis, maritime shipping is 14% more energy-efficient than rail transportation, and 594% more energy-efficient than trucking. Continued investment and renewal in Great Lakes and Seaway vessel fleets is expected to further improve the comparative efficiency of the shipping mode. These efficiency benefits also mean that, on a ton-per-mile basis, rail emits 19% more and trucking emits 533% more greenhouse gas emissions (GHG) than MTS shipping.

While shipping is more energy efficient than other modes of transportation with lower GHG and nitrogen oxides (NOX) than other modes, it has historically been a relatively higher emitter  per ton-mile of sulfur oxides (SOX) and particulate matter (PM) (see the 2011 study by the Research and Traffic Group). Additional work is being done to further reduce the air emissions associated with vessel operations. Much of this work is being guided by international regulations related to air emissions.

The International Maritime Organization (IMO) has established global standards for ship-related pollution, referred to as the International Convention for the Prevention of Pollution from Ships(MARPOL). In 2005, MARPOL Annex VI entered into force. This regulation sets limits on NOx and SOX emissions and allows for the creation of Emission Control Areas (ECA), which have more stringent emission standards than the Annex VI requirements.

In 2010, the IMO designated the North American ECA, which further limited emissions for all vessels operating in waters off of Canada and the United States, including waters in the Great Lakes-St. Lawrence River MTS. In particular, this ECA limits the amount of sulfur that may be present in vessel fuels, and the amount of NOX that can be emitted. Selected exemptions were made for Great Lakes steamships (vessels powered by boilers), which have a longer time period to meet compliance requirements and are often being re-powered with new internal combustion engines instead. Vessels with exhaust scrubber systems capable of removing SOX are also exempt from the fuel requirement. In the United States, the U.S. Environmental Protection Agency implemented ECA-relevant regulations. Transport Canada implemented ECA-relevant regulations in Canada.

To further reduce fuel consumption and emissions and comply with the stringent emission regulations of the North American ECA, U.S. and Canadian vessel owners have been investing in new engines, exhaust treatment systems, and entirely new vessels.