We use four stream segments along a wood-rich, pool-riffle mountain stream in the Southern Rockies of Colorado, USA to examine how spatial variations in wood load and variations in discharge during and after the snowmelt peak flow influence the magnitude of surface and subsurface transient storage. Segments range in complexity from a single channel with no large wood to an anabranching channel with closely spaced, channel-spanning logjams. Discharges at which transient storage was assessed range from base flow to snowmelt peak flow. To explore these relations, we used 10 geomorphic variables representing channel morphology and bed substrate, four wood-related variables representing wood load and associated backwater storage, and two measures of skewness from instream and bulk electrical conductivity breakthrough curves during tracer tests. Instream curves reflect surface and subsurface transient storage, whereas bulk curves primarily represent subsurface transient storage. Higher values of skewness indicate greater retention, and we used the values here as a metric of increased transient storage. Although limited sample size restricts the power of our results, our findings suggest that stream segments with greater instream large wood loads have more and larger pools, greater storage of fine sediment and particulate organic matter, and higher values of skew from instream conductivity. The results also suggest that the presence of instream wood, rather than changes in channel morphology associated with wood, is the most important driver of transient storage. This implies that river management designed to foster transient storage should focus on retaining instream large wood. We did not find significant correlations between geomorphic or wood-related variables and the skew estimated from bulk conductivity, which may reflect the relatively thin alluvium present in the field area and the prevalence of surface transient storage in this system.