Aquatic vegetation is a critical component of nursery habitat for young-of-the-year (YOY) muskellunge. The trophy status of the muskellunge fishery in southeastern Georgian Bay owes its reputation to the widespread distribution of aquatic vegetation in coastal marshes of this region. Unfortunately, wetland habitat has been in decline because of an unprecedented period of sustained low water levels since 1999. In this study, we strategically resampled 16 historic sites that supported YOY muskellunge in 1981. The sustained low water levels and increased shoreline modifications experienced by southeastern Georgian Bay may have contributed to the current disappearance of YOY muskellunge at those sites. These physical stressors appeared to have altered the habitat structure of the plant community and led to changes in fish communities, making them no longer suitable for YOY muskellunge. The precise mechanisms limiting survival to the YOY stage are unknown because spawning adults have been observed in the area in the spring of 2012 and 2013. These results corroborated previous sampling programs at the historic sites (2004–2005: n = 8 and 2007: n = 16) that employed other fishing gears and protocols as well as a supplemental YOY sampling in 2013 (n = 26 additional sites). If this muskellunge population is to remain self-sustaining, a complementary management strategy specifically developed for Georgian Bay is required. The strategy should identify and ultimately protect suitable muskellunge breeding habitat by accounting for the unique geomorphology, current physical stressors affecting Georgian Bay, and the biological links between suitable spawning and nursery habitats.