Exotic species are associated with a variety of impacts on biodiversity, but it is unclear whether impacts of exotic species differ from those of native species with similar growth forms or native species invading disturbed sites. We compared presence and abundance of native and exotic invaders with changes in wetland plant species diversity over a 28-year period by re-surveying 22 ponds to identify factors correlated with observed changes. We also compared communities found within dense patches of native and exotic emergent species with similar habits. Within patches, we found no categorical diversity differences between areas dominated by native or exotic emergent species. At the pond scale, the cover of the exotic grass Phragmites australis best predicted change in diversity and evenness over time, likely owing to its significant increase in coverage over the study period. These changes in diversity and evenness were strongest in younger, less successionally-advanced ponds. Changes associated with cover of P. australis in these ponds were not consistent with expected diversity decreases, but instead with a dampening of diversity gains, such that the least-invaded ponds increased in diversity the most over the study period. There were more mixed effects on evenness, ranging from a reduction in evenness gains to actual losses of evenness in the ponds with highest invader cover. In this wetland complex, the habit, origin and invasiveness of species contribute to diversity responses in a scale- and context-dependent fashion. Future efforts to preserve diversity should focus on preventing the arrival and spread of invaders that have the potential to cover large areas at high densities, regardless of their origin. Future studies should also investigate more thoroughly how changes in diversity associated with species invasions are impacted by other ongoing ecosystem changes.