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Stream mesoscale habitats have systematic topographic relationships to hyporheic flow patterns, which may create predictable temperature variation between mesoscale habitat types. We investigated whether systematic differences in temperature metrics occurred between mesoscale habitats within reaches of small streams tributary to the upper Little Tennessee River, southern Appalachians. Surface water temperature was recorded over three or four mid-summer days in four mesoscale habitat types: riffle, main riffle, pool and alcove in 44 stream segments (sites). Temperature metrics were calculated for each mesoscale habitat relative to the mean value of the metric over the stream: Δ maximum temperature, Δ average maximum temperature and Δ maximum daily variation and also for each site: standard deviation of the maximum temperature and average diurnal variation (ADV). Sites were categorized as fully or partially forested. Pool tailouts had statistically significantly lower Δ maximum temperature and Δ average maximum temperature than riffle tailouts in partially forested sites, although differences were small. This was the opposite of what was expected in the presence of hyporheic exchange, indicating hyporheic exchange is not a dominant driver of mesoscale habitat temperatures at these sites. Temperature differences between mesoscale habitat units were small and unlikely to have ecological significance. We also evaluated relationships between stream temperature and riparian condition, watershed % impervious surfaces, watershed % non-forested and elevation. ADV and standard deviation of the maximum temperature were significantly higher in partially forested sites, indicating that partially forested sites have greater temperature ranges and spatial variation of maximum temperatures. ADV decreased with elevation and increased with % impervious surfaces. Copyright © 2013 John Wiley & Sons, Ltd.