Submerged aquatic vegetation (SAV) plays several crucial ecological roles and provides invaluable ecosystem services to humans. However, it is declining globally, principally due to an increase in the amount of suspended matter and nutrients within water bodies. A series of studies of the SAV in Lake Saint-Pierre (Québec, Canada) conducted between 2002 and 2021, documented changes in the occurrence and species composition of this vegetation type. The probability of observing SAV at the different sampling stations decreased from 75% in 2002 to 20% in 2021. This decline was accompanied by a change in species composition, mainly associated with a decrease in the amount of American eelgrass (Vallisneria americana). The clearer mass of water flowing from the Great Lakes possibly offers a photic refuge for SAV in Lake Saint-Pierre. Any intervention that would potentially reduce the dispersion of this water mass within the lake should be avoided. Management actions aimed at improving the water quality of Lake Saint-Pierre and its tributaries, notably by reducing turbidity, are needed to restore and protect this UNESCO World Biosphere Reserve.