Rivermouths are dynamic systems characterized by hydrologic mixing, where water, energy, sediment and nutrients from both river and receiving water unite to form a unique yet variable environment. Water levels in these environments are thus defined by, and subject to, streamflow from the river and lake-level fluctuations. Long-term fluctuations in water levels affect hydrogeomorphic structure, as well as wetland structure, distribution, and composition. A better understanding of these dynamics will help us to comprehend the processes that govern changes in wetland area and, thus, the breadth of the ecosystem services that estuarine wetlands provide. To this end, this study examined how wetland plant communities have changed through time in relation to long-term changes in water levels from both river and lake systems, using historic aerial photograph interpretation in three rivermouths on Lake Michigan. Additionally, the observed patterns of historic water levels and streamflows were used to inform our predictions for the future in light of climate changes. Results showed that higher water levels and peak streamflows led to less wetland area; average streamflow did not play a statistically detectable role in rivermouths that had lake-dominated morphologies but was significant in the rivermouth system that was riverine dominated. This suggests that varying rivermouth morphologies respond differently to lake and stream dynamics. Restoration decisions that take rivermouth morphology into account will be important as these systems continue to change both naturally and due to climate or other anthropogenic disturbances. It is important to realize not only the extent to which humans are affecting rivermouth systems, but also the interplay between water levels, streamflows, hydrogeomorphology, and wetland ecology within these systems themselves, so as to better understand the necessary steps for restoration.