In this report, we describe how aspects of existing freshwater mussel indices of biological integrity can be modified to fit within the planning paradigm established for developing and certifying ecological models for U.S. Army Corps of Engineers’ planning purposes. Herein, we present examples of using freshwater mussels for biological monitoring, how to calculate their associated IBIs specific to their region of origin and their potential use in ecosystem restoration planning. Additionally, we present general conceptual models that may be used in ecological model development and environmental benefits analysis for projects that focus on freshwater mussel habitat restoration.