The U.S. Army Corps of Engineers (USACE) Jacksonville District plans to deepen 13 miles of the lower St. Johns River (LSJR) federal channel for larger vessels. USACE retained Taylor Engineering to perform ecological modeling to assess potential impacts of the channel deepening. Taylor Engineering used models of five ecosystem components (submerged aquatic vegetation, benthic invertebrates, fish, wetlands, and phytoplankton) developed by the St. Johns River Water Management District (SJRWMD) specifically for the LSJR and, where necessary, developed additional analyses to augment the SJRWMD models. The ecological models assessed the effects of salinity changes with different channel depths to identify the project design that best meets engineering and economic criteria, avoids and minimizes environmental impacts, and mitigates for unavoidable impacts as required by the National Environmental Policy Act (NEPA). The models used the results of 3-D hydrodynamic / salinity models of the river (also developed by Taylor Engineering) in spreadsheet and GIS (ArcMap) analyses to identify salinity characteristics that affect the size and spatial distribution of ecological communities under different channel design scenarios. Taylor Engineering hosted interagency meetings to brief state and federal agencies on the project and participated in USACE public presentations. Taylor Engineering completed the work within an aggressive schedule necessitated by the project’s inclusion in the President’s “We Can’t Wait” economic initiative.