The declining condition of river systems associated with rapid development of human societies has led to substantial declines in fish diversity. One cause of decline is the loss of in-stream Structural Woody Habitat (SWH), an important component of stream ecosystems, particularly as fish habitat. As a result there has been an increase in the number of rehabilitation programs that introduce SWH into rivers. This paper assesses fish responses to SWH introduction in riffles and pools in the Hunter River, eastern Australia, using a Multiple-Before-After-Control-Impact (MBACI) experimental and analytical design. In the riffle experiment, species richness was comparable among all control and treatment riffles across the entire study period. However, there were significant differences in assemblage structure, fish abundance, and biomass between control and treated riffles. The introduction of SWH (bank embedded deflector jams) appeared to create additional habitat which was utilized by one native fish species (Retropinna semoni—Australian smelt) and one alien species (Gambusia holbrooki—mosquito fish). In pools there were no significant changes in fish species richness, abundance, or biomass following introduction of SWH (pool jams). These findings have important practical and cost implications in terms of the design and implementation of rehabilitation strategies using SWH to restore fish assemblages in degraded streams.