Restoring industrialized Great Lakes estuaries requires approaches that maintain navigation while addressing decades of ecological degradation. One increasingly used strategy is the beneficial use of clean dredged material for aquatic habitat restoration, yet evaluating its ecological effectiveness remains challenging due to geomorphic heterogeneity, variable exposure regimes, and inconsistent analytical frameworks. This dissertation evaluates the use of clean dredged material across diverse aquatic habitats using the St. Louis River Estuary (SLRE) as a decision laboratory. To support consistent and management of relevant evaluation, I developed the Aquatic Habitat Evaluation of Restoration Success Tool (AqHERST), a reproducible, analytical framework that integrates 31 years of benthic monitoring data. AqHERST compares preconstruction and post construction conditions to least-impaired, geomorphic zone-specific reference distributions using nonparametric statistical tests. Although the framework accommodates multiple ecological metrics, this dissertation focuses on two benthic macroinvertebrate indicators: the scaled Trimetric Index (s-TMI), which serves as the primary measure of benthic condition, and the scaled Hexagenia Density Index (s-HDI), which functions as a sensitivity indicator linked to sediment stability and contaminant stress. These biological indicators are interpreted alongside physical context metrics, including relative exposure index, and supported by spatial visualization using graduated color maps. Together, this integrated approach identifies where restoration design elements effectively address dominant stressors and where physical setting constrains recovery. Application of AqHERST across eight restoration projects in the SLRE demonstrates a consistent pattern. When placement, bathymetry, and exposure management are aligned with geomorphic-zone context, clean dredged material produces measurable and statistically defensible improvements in benthic condition. In contrast, projects located in higher exposure; urbanized settings exhibit slower recovery trajectories, indicating the need for additional stabilization measures or longer maturation periods. Overall, this dissertation demonstrates that geomorphic zone-specific target setting, standardized statistical evaluation, and spatial visualization can transform heterogeneous monitoring data into actionable restoration decisions. The results show that clean dredged material can be an effective tool for aquatic habitat restoration in Great Lakes estuaries when placement and design are co-optimized with physical setting, supporting both Beneficial Use Impairment removal and long-term adaptive management.