Coves are part of the mosaic of fish habitats in many U.S. reservoirs, but over time these coves may be disconnected from the main reservoir for varying durations due to the buildup of sediment berms at the mouth that are higher than reservoir elevations. Our 4-year study (2017-2020) of five coves in Harlan County Reservoir, Nebraska, across three seasons (spring, summer, and fall) provided an opportunity to compare fish communities between coves that have remained connected to the main body of the reservoir and coves that have been intermittently connected to or disconnected from the reservoir over the past 10 years. Further, we were able to evaluate fish community changes in coves following substantial flood events in 2019 that reconnected all disconnected coves to the main body of the reservoir. Taxonomic richness and diversity were lower in the intermittently connected and disconnected coves compared to the connected coves in 2017 and 2018. Only Common Carp Cyprinus carpio were found in the disconnected cove, and Black Bullheads Ameiurus melas were only found in intermittent coves. However, fish communities notably shifted in intermittently connected and disconnected coves after the reconnection event in 2019 and became more similar to those in connected coves. Most notably, species richness in the disconnected cove increased from 1 species preconnection to 18 species postconnection, and two new species (Flathead Catfish Pylodictis olivaris and Golden Shiner Notemigonus crysoleucas) were found in at least one cove type during the postflood period that had not been present in any coves prior to the connection. Results from this study underscore the importance of coves as habitats for some species and provide insights as to how fish communities may change when coves are reconnected, whether by human intervention or variations in reservoir elevation.