Great Lakes coastal wetlands are subject to water level fluctuations that promote the maintenance of coastal wetlands. Point au Sauble, a Green Bay coastal wetland, was an open water lagoon as of 1999, but became entirely vegetated as Lake Michigan experienced a prolonged period of below-average water levels. Repeat visits in 2001 and 2004 documented a dramatic change in emergent wetland vegetation communities. In 2001 non-native Phragmites and Typha were present but their cover was sparse; in 2004 half of the transect was covered by a 3 m tall, invasive Phragmites and non-native Typha community. Percent similarity between plant species present in 2001 versus 2004 was approximately 19% (Jaccard's coefficient), indicating dramatic changes in species composition that took place in only 3 years. The height of the dominant herbaceous plants and coverage by invasive species were significantly higher in 2004 than they were in 2001. However, floristic quality index and coefficient of conservatism were greater in 2004 than 2001. Cover by plant litter did not differ between 2001 and 2004. The prolonged period of below-average water levels between 1999 and early 2004 exposed unvegetated lagoon bottoms as mud flats, which provided substrate for new plant colonization and created conditions conducive to colonization by invasive taxa. PCR/RFLP analysis revealed that Phragmites from Point au Sauble belongs to the more aggressive, introduced genotype. It displaces native vegetation and is tolerant of a wide range of water depth. Therefore it may disrupt the natural cycles of vegetation replacement that occur under native plant communities in healthy Great Lakes coastal wetlands.