Abstract Predicting how stream fishes may respond to habitat restoration efforts is difficult, in part because of an incomplete understanding of how basic biological parameters such as growth and ontogenetic habitat shifts interact with flow regime and riverscape ecology. We assessed age-specific Guadalupe Bass Micropterus treculii habitat associations at three different spatial scales in the South Llano River, a spring-fed stream on the Edwards Plateau of central Texas, and the influence of habitat and flow regime on growth. We classified substrates using a low-cost side-scan sonar system. We used scale microstructure to determine age and to back-calculate size at age. Over 65% of captured Guadalupe Bass were age 2 or age 3, but individuals ranged from 0 to 7 y of age. Habitat associations overlapped considerably among age classes 1–3+, but age-0 Guadalupe Bass tended to associate with greater proportions of pool and run mesohabitats with submerged aquatic vegetation. Although habitat metrics across multiple scales did not have a large effect on growth, river discharge was negatively correlated with growth rates. Understanding age-specific Guadalupe Bass habitat associations at multiple scales will increase the effectiveness of restoration efforts directed at the species by assisting in determining appropriate ecological requirements of each life-history stage and spatial scales for conservation actions.