Armoring involves the placement of erosion resistant materials (e.g., large rocks and boulders, cement, pilings, and large woody debris) or the use of bioengineering techniques along shorelines, streambanks, or in other areas of high flow velocities and/or wave-tidal energy to reduce or eliminate erosion of natural shorelines and risk to human infrastructure. Unfortunately, altering the physical conditions of the streambank or shoreline through armoring, or bank stabilization, can radically alter the local characteristics of natural habitats and may influence the habitat for some distance surrounding the structure. Bank stabilization also affects natural channel processes that are essential to habitat creation and maintenance. As a result, the ecological functions of the impacted area can be altered, including the use of these habitats by fish, macroinvertebrates, birds, and other organisms. Conceptual models are used to organize available information relative to ecosystem impacts. This conceptual model and accompanying text outline relationships between shoreline modification techniques; the physical, chemical, and biological processes and functions of freshwater systems; and the potential impacts to salmonid fitness at both large (reach level) and small (site level) scales. Particular emphasis is placed on the evaluation of effects on salmonid species and their essential habitat.