Shipping is a major economic activity on the St. Lawrence, but there is a serious pollution risk involved. The wave action caused by ships and deballasting are sources of stress on the River's ecosystem. In addition, several hundred thousand cubic metres of sediment have had to be dredged from the Seaway each year since 1989 to serve shipping. Some of the best farmland in Quebec lies along the banks of the St. Lawrence. However, the intensification of agricultural practices since the early 1960s has become a problem.
Agricultural pollution comes from non-point sources, making it difficult to quantify.
The intensive use of fertilizers and pesticides and erosion of farmland along the River is cause for concern for the St. Lawrence ecosystem. One-third of the River's wetlands were lost to farming between 1945 and 1976. The power generation industry has had a major impact on the environment. Hydroelectric dams cause major changes to the aquatic ecosystem, while conventional and nuclear thermal power plants require high volumes of water for cooling and their discharges increase water temperature, which can have a harmful effect on the environment. Commercial fishing helps drive the economy of the Gasp , Magdalen Islands and Lower North Shore.