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.

The stocking of fishes outside of their native range for the purpose of sport fisheries can lead to secondary contact and introgression between species that were historically allopatrically distributed. Smallmouth Bass Micropterus dolomieu were introduced within the range of Guadalupe Bass M. treculii in central Texas and introgressive hybridization subsequently occurred. One recent survey of temporal changes in introgression in the Blanco River found that introgression had increased and that Guadalupe Bass had been extirpated. Thus, a survey of changes in introgression across the range of the Guadalupe Bass was conducted in 12 subbasins in the Brazos, Colorado, Guadalupe–San Antonio, and Nueces drainages in Texas using 15 microsatellite loci. The results indicate that introgression is now occurring in four subbasins but no longer occurring in the Lampasas and San Gabriel rivers, where rates were previously 6% and 46%, respectively. Additionally, we found no evidence that stocking of hatchery‐reared individuals in the Guadalupe and Nueces rivers has led to severely depressed genetic variation. The variable success of restoration efforts to prevent extirpation of the Guadalupe Bass suggests that protection of the remaining nonintrogressed populations should be a priority for the conservation of this species.

The Guadalupe bass Micropterus treculii is endemic to Texas and is threatened by introgression with introduced smallmouth bass M. dolomieu as well as habitat degradation. This study described and quantified the movements and habitat associations of Guadalupe bass to assess the factors that may influence current populations. Radio-tagged adult Guadalupe bass were tracked in the Pedernales River (n ¼ 12) and South Llano River (n ¼ 12) from January through August 2008. Available microhabitats were measured and modeled in terms of depth, velocity, substrate, and cover for about 1.5 km in the Pedernales River and 1.2 km in the South Llano River. Rates of movement were greatest during the reproductive season, ranging from less than 1 to 9 m/d. Instream cover (such as undercut banks and woody debris) was preferred during daylight hours throughout the study period, although the distances from cover increased from January to August. Habitat shifts from cover to open water occurred at night and from woody structures to boulders and ledges during a large flood pulse. The habitats most suitable for adult Guadalupe bass had a depth of 1.0 m and a current velocity of 0.05 m/s, and habitat selection was strongest for eddy mesohabitats with smaller substrates. By July, the Guadalupe bass in the South Llano River were associated with runs with greater current velocities, whereas those in the Pedernales River were associated with pools with greater depths, largely owing to the low flows and reduced habitat availability in the Pedernales River. Environmental factors, including the availability and suitability of instream cover, are probably the strongest influences on the distribution and abundance of Guadalupe bass.

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