AbstractCoarse woody habitat (CWH) in aquatic ecosystems provides structural complexity and a surface for food production for fish. Depending on abundance and complexity of CWH, it is usually associated with influencing predator–prey dynamics, fostering greater localized fish abundance, increasing fish growth, and contributing to fish production, but some conflicting evidence exists about its importance as fish habitat. Our experiment was designed to test for direct linkages between whole‐lake CWH availability and fish community abundance, biomass, and production. We removed ~50% of CWH from three lakes while concurrently sampling them and two other unaffected lakes as controls in a before‐after–control‐impact (BACI) design. Due to the loss of quality foraging habitat, structure, and cover for small fish, we hypothesized that the CWH removal would cause a measurable decline in fish abundance, biomass, and/or production. Despite CWH being a preferred habitat type for fish, our hypothesis was not supported because observed changes in measured fish community metrics could not be attributed to the CWH removal. The inability to directly link the wood removal to changes in the fish metrics we examined may have been due to a number of factors including the composition of the fish community, the high availability of alternate habitat structure (rocks, macrophytes), large quantities of wood remaining in the lakes, the relative lack of littoral habitat use by piscivores, or low statistical power (small sample size, high variance). However, we still urge resource managers to be cautious when considering authorizing removal of CWH from lakes because it does provide temporally stable year‐round structure and high‐quality foraging habitat with unique microbial, fungal, and invertebrate communities. Coarse woody habitat was a preferred habitat for fish and may have a greater relative importance in lakes with minimal alternative cover for fishes or in lakes containing different fish assemblages.