Abstract: The lower Mississippi River (LMR) has been heavily modified for multiple human purposes such as navigation, flood control, and bank stabilization. However, the LMR simultaneously supports a diverse fish fauna that includes recreational and commercial fisheries. Due to river training and diversion structures constructed during the past 80 years, the historic characteristics of the LMR have been drastically altered and have likely influenced fishes and fisheries in the system. One common restoration measure used throughout the LMR has been to " notch” wing-dike structures that close secondary (side) river channels. Dike notching allows year-round flows through secondary channels, which enhances habitat diversity and promotes biological productivity at the ecosystem scale. Although notching is presumed good for LMR fishes and other biota, few studies have examined its effects on fish assemblages. In this study, fish assemblages were sampled at seven LMR secondary channels spanning from river kilometer (rkm) 628 (Louisiana-Mississippi, U.S.A.) upstream to rkm 1504 (Missouri-Kentucky, U.S.A.). Four secondary channels were termed " permanent” (i.e., with notched dikes) while three secondary channels were termed " temporary” (i.e., without notched dikes). Fishes were sampled by boat-mounted electrofishing conducted during falling and low stages from 1995—1997. Fish assemblages differed between permanent and temporary secondary channels, and varied somewhat between falling and low stages. Gizzard shad (Dorosoma cepedianum), threadfin shad (D. petenense), and white bass (Morone chrysops) demonstrated consistent preferences for low-current conditions associated with temporary secondary channels. Conversely, blue catfish (Ictalurus furcatus), flathead catfish (Pylodictis olivaris), and freshwater drum (Aplodinotus grunniens) were more associated with permanent secondary channels. Future restoration strategies in the LMR should consider dike notching and resultant maintenance of permanent secondary channels in selected river reaches. However, temporary secondary channels also contain unique fish species, and also appear to be important sites of riverine primary production. Restoration strategies should consider a balance of both secondary channel types, which should support the greatest biodiversity for the LMR ecosystem.