Coastal wetlands occur throughout the Laurentian Great Lakes where hydrology and sediment are conducive to macrophyte growth. These shallow, productive ecosystems have diverse emergent and submergent vegetation that provides critical habitat for many species of fish, birds, mammals, reptiles, and amphibians. Unfortunately, approximately half of the coastal wetland area that was present before European settlement has been converted to other land uses and the majority of remaining wetlands are impacted to varying degrees by invasive species, fragmentation, nutrient loading, and hydrologic manipulation. Consequently, coastal wetland protection and restoration are vital components of a long‐term management strategy for the Great Lakes. For protection and restoration to be effective, however, a better understanding of coastal wetland structure and function and improved monitoring tools are needed. In my research, I found that watershed and surrounding land cover, especially agriculture, impacted coastal wetland water quality by increasing nutrient concentrations, conductivity, and turbidity. Using nutrient-diffusing substrata, I found that algal biomass accrual was frequently nitrogen-limited and rarely phosphorus-limited, suggesting that nitrogen loading from agricultural lands and other sources has the potential to stimulate excessive algal growth and affect ecosystem function in Great Lakes coastal wetlands. I also documented water quality impairment and altered land cover to be associated with structural changes to algal, macroinvertebrate, and fish communities, illustrating the far-reaching impacts of anthropogenic disturbance on coastal wetland ecosystems. Macroinvertebrate community structure was also related to natural drivers including hydrologic energy and water levels. I used my findings related to abiotic conditions and community structure to develop a fish-based index of biotic integrity and an abiotic index of wetland conditions for use in monitoring. These tools will help ecosystem managers to track wetland conditions and to prioritize protection and restoration investments across the Great Lakes basin. Furthermore, given that these anthropogenic stressors and natural drivers are not unique to the Great Lakes, my findings and related indices are applicable to other coastal ecosystems.