1. Habitat heterogeneity at multiple scales is a major factor affecting fish assemblage structure. However, assessments that examine these relationships at multiple scales concurrently are lacking. The lack of assessments at these scales is a critical gap in understanding as conservation and restoration efforts typically work at these levels.2. A combination of low-cost side-scan sonar surveys, aerial imagery using an unmanned aerial vehicle, and fish collections were used to evaluate the relationship between physicochemical and landscape variables at various spatial scales (e.g. micro-mesohabitat, mesohabitat, channel unit, stream reach) and stream-fish assemblage structure and habitat associations in the South Llano River, a spring-fed second-order stream on the Edwards Plateau in central Texas during 2012-2013.3. Low-cost side-scan sonar surveys have not typically been used to generate data for riverscape assessments of assemblage structure, thus the secondary objective was to assess the efficacy of this approach.4. The finest spatial scale (micro-mesohabitat) and the intermediate scale (channel unit) had the greatest explanatory power for variation in fish assemblage structure.5. Many of the fish endemic to the Edwards Plateau showed similar associations with physicochemical and landscape variables suggesting that conservation and restoration actions targeting a single endemic species may provide benefits to a large proportion of the endemic species in this system. 6. Low-cost side-scan sonar proved to be a cost-effective means of acquiring information on the habitat availability of the entire river length and allowed the assessment of how a full suite of riverscape-level variables influenced local fish assemblage structure.