Abstract: Six ecosystem models were developed to evaluate restoration measures for the Lower Mississippi River Resource Assessment that considered connectivity between river and floodplain, substrate quality in riverine habitats, and targeted species of special interest including Paddlefish and wetland fish assemblages. A total of 85 restoration measures in the Hatchie to Loosahatchie reach were identified by the Project Delivery Team that had different modeling requirements. Field data collected by the Engineer Research and Development Center–Environmental Laboratory in the Lower Mississippi River and floodplain identified ecological guilds of fish and aquatic invertebrates representative of different fluvial habitats. Regression and frequency bar chart models developed from this database predicts a biotic response as a function of habitat quality. Six models applicable to either riverine (unidirectional flow) or floodplain (bidirectional flow) environments were used to evaluate measures for enhancing benthic substrates, reestablishing woody debris, and formation of eddies to diversify habitat. Outputs were normalized as a Habitat Suitability Index on a 0–1 scale and a spreadsheet developed to calculate and annualize Habitat Units for selected restoration measures. Models were certified by US Army Corps of Engineers National Ecosystem Restoration Planning Center of Expertise for regional use in the Lower Mississippi River.