Aquatic vegetation in the relatively pristine coastal wetlands of eastern Georgian Bay provides critical habitat for a diverse fish community. Declining water levels in Lake Huron over the past decade, however, have altered the wetland plant assemblages in favour of terrestrial (emergent and meadow) taxa and have thus reduced or eliminated this important ecosystem service. In this study, we compared IKONOS satellite images for two regions of eastern Georgian Bay (acquired in 2002 and 2008) to determine significant changes in cover of four distinct wetland vegetation groups [meadow (M), emergent (E), high-density floating (HD) and low-density floating (LD)] over the 6 years. While LD decreased significantly (mean −2995.4 m2), M and HD increased significantly (mean +2020.9 m2 and +2312.6 m2, respectively) between 2002 and 2008. Small patches of LD had been replaced by larger patches of HD. These results show that sustained low water levels have led to an increasingly homogeneous habitat and an overall net loss of fish habitat. A comparison of the fish communities sampled between 2003 and 2005 with those sampled in 2009 revealed that there was a significant decline in species richness. The remaining fish communities were also more homogeneous. We suggest that the observed changes in the wetland plant community due to prolonged low water levels may have resulted in significant changes in the fish communities of coastal wetlands in eastern Georgian Bay.