Effective management of wetlands often involves the suppression of invasive species, and understanding the ecological consequences of management efforts is an important goal. A non-native strain of Phragmites australis (Common Reed; hereafter Phragmites) is aggressively invading North American wetlands, and the species has been shown to alter hydrology and impact aquatic organisms. Clear Creek Wildlife Management Area, in Kentucky, is heavily impacted by Phragmites invasion. Portions of the Wildlife Management Area with Phragmites were treated with herbicide to restore wetland flora, and in this study, we evaluated the effects of both the presence and management of Phragmites on wildlife populations and ecosystem function. We selected 3 locations (treated Phragmites, untreated Phragmites, and Phragmites-free) and surveyed each for water chemistry, wildlife populations, and stable-isotope signatures over a 2-y period. Water chemistry varied with the presence or absence of Phragmites, suggesting differences in nutrient cycling. Fish diversity did not differ among sites, but individual species varied in distribution and abundance between the Phragmites sites and the Phragmites-free site. Turtles showed significant differences in both diversity and body size based on the presence or absence of Phragmites, but not herbicide treatment. We detected no significant differences in frog diversity across treatments. We recorded 8 Kentucky Species of Greatest Conservation Need, but there were few differences in the distribution of these species across sites. Stable-isotope analysis revealed variation in food-web structure based on the presence of Phragmites. These results indicate that herbicides had little effect on fish and herpetofaunal communities in the short term, but potentially significant ecological changes may occur if Phragmites were eradicated. Our conclusions highlight the importance of monitoring habitat restoration to guide future management. A holistic, ecosystem-level approach is necessary to understand the impacts of both invasive species and their management.