The Upper Mississippi River is maintained in its current navigable state through impoundments, dredging, and other engineering projects. These stressors, along with anthropogenic impacts and natural system processes, led to declines in aquatic vegetation and the loss of fish and wildlife habitat, with a major downturn the late 1980s and early 1990s. Large‐scale restoration projects, such as the one evaluated here, are primarily designed to rehabilitate and enhance fish and wildlife habitat. We determined whether an individual restoration project, construction of an island complex, fulfilled a programmatic goal of re‐establishing diverse and abundant native aquatic vegetation. Eighteen years of aquatic vegetation monitoring data from impact and reference areas were compared to evaluate the anticipated direct effects (within 400 m of the constructed islands) and indirect effects (>400 m downstream of constructed islands) of restoration. Impact areas were also compared with an unrestored negative reference area ~200 km downstream of the project and with a positive reference area in adjacent, relatively natural backwaters. Only indirect effects of restoration were evident. Prevalence and species richness of aquatic vegetation in both of the impact areas and in the negative reference area increased prior to restoration, suggesting large‐scale improvement independent of the project examined here. Indirect effects were demonstrated as further increases in both prevalence and species richness coinciding with restoration in the area >400 m downstream of the restoration. We conclude that increased abundance and diversity of aquatic vegetation was partially achieved, with observed improvements potentially linked to reduced wind fetch.