Submerged aquatic vegetation (SAV) distribution and coverage were quantified in two bays of Lake Ontario in 1972, 1980 (1982), and 1999–2002, using a combination of aerial photograph interpretation (API), hydroacoustics, and rake sampling. The three methods gave similar estimates of SAV presence in 2002, supporting our use of API for quantifying SAV changes across decades in bays of a large lake. The SAV coverage in Sodus Bay increased by 5% between 1972 and 1980 and by 35% between 1980 and 1999–2002 whereas the maximum depth of SAV colonization extended from 5.5 to 6.4 m during this period. In Chaumont Bay, the SAV coverage tripled while its maximum depth of occurrence increased from 5.1 to 6.1 m from 1982 to 2002. Although the difference in SAV coverage between 1972 and 1980 was not larger than the difference between consecutive years in the 2000s, the large increase in SAV coverage between the 1980s and 2000s represents a major ecosystem change in these bays. This change was likely caused by increased water clarity in Lake Ontario, which could be associated with the implementation of the Great Lakes Water Quality Agreement (GLWQA) and the dreissenid mussel invasion. Although other factors such as water level, wave exposure, bottom slope, and sediment nutrients may be important, they have not changed in a fashion that would predict local increases of SAV coverage.