Many Great Lakes coastal wetlands have been impounded (diked) to provide protection from flooding and to manipulate water levels for vegetation management. Dikes change the hydrological regime by isolating the coastal wetland from natural lake processes. We evaluated the seed bank composition of seven pairs of diked and undiked coastal wetlands in Green Bay (Lake Michigan) and Saginaw Bay (Lake Huron) to assess the effects of dikes on vegetation dynamics. We also compared soil pH, organic matter, total N, P and K between diked and undiked wetlands. On average, substrates of diked wetlands contained almost three times as many seeds as in undiked wetlands and approximately 20% more species. Seed banks of diked wetlands contained greater numbers of seeds from mudflat aquatic species, whereas seed banks of undiked wetlands yielded greater numbers of seeds from sandy/shoreline species. Diked wetland soils were more acidic, had higher organic matter content, and higher total N, P and K levels compared with soils in undiked wetlands. Our results suggest that diked wetlands may be “traps” for high levels of nutrients, organic matter and seeds. At the sites in this study, construction of dikes appears to have transformed coastal wetlands into systems that function more like inland wetlands.