In shallow reservoirs, seasonal water drawdowns expose littoral areas and over time produce barren mudflats. When flooded, mudflats provide homogeneous substrates, turbid water, and eroding shorelines of limited ecological value. We hypothesized that in mudflats structurally complex habitats are occupied by more fish, smaller fish of a larger range in sizes, more species, and fish assemblages that are different from those in simpler habitats. We tested these hypotheses over two consecutive years with fish collections made in sites with varying structural complexity. Results indicated that structural complexity harbors more fish in transects and enclosures. Structural complexity did not influence median length, but length range increased with structural complexity. Average species richness increased with structural complexity. Fish assemblage composition changed as structural complexity increased. The ability of cover to provide survival, growth, and carrying capacity benefits is fundamental to programs aimed at increasing structural complexity. Results suggest observed effects on fish assemblages can lead to such benefits. Considering mudflats are a major component of reservoirs, expand as reservoirs age, and there is a potential to exert meaningful change on fish assemblages of impounded rivers by managing mudflats, we suggest additional attention is needed to develop practical habitat restoration options.