The spatiotemporal patterns and ecological significance of the retention of coarse particulate organic matter and large woody debris have been intensively studied in perennial rivers and streams but are virtually unknown in ephemeral systems. We examined the influence of 2 features characteristic of ephemeral systems, downstream hydrologic decay and in-channel tree growth, on the distribution, transport, and retention of woody debris following a flood having a ∼2.6-y recurrence interval in the ephemeral Kuiseb River in southwestern Africa. A total of 2105 pieces of wood were painted at 8 sites along the river channel to measure retention patterns. The flood had a peak discharge of 159 m³/s at the upper end of the study area, decaying to <1 m³/s by 200 km downstream. Downstream export of wood from marking sites totaled 59.5% (n = 1253). Transport distances ranged from 1 to 124 km, and 34.8% (n = 436) of the exported wood was recovered. Marked wood retained within marking sites was significantly longer than exported wood (p < 0.001, t-test). Once in transport, there was little correlation between wood length and distance traveled (r = 0.11, correlation analysis, n = 369). Length influenced the site of retention; material retained on debris piles was significantly longer than that stranded on channel sediments (p < 0.001, t-test). In-channel growth of Faidherbia trees significantly influenced wood retention; 83.7% of marked wood not moved by the flood was associated with debris piles on Faidherbia trees. Similarly, 65% of the exported wood retained within downstream debris piles was associated with Faidherbia trees. In contrast to many perennial systems, we observed a general increase in wood retention downstream, peaking in the river's lower reaches in response to hydrologic decay. Debris piles induced sediment deposition and the formation of in-channel islands. Following flood recession, debris piles and their associated sediments provided moist, organic-rich microhabitats, which were focal points for decomposition and secondary production, mimicking patterns reported from the channels of perennial streams and rivers. The ecological significance of retentive obstacles and associated organic debris is a feature common to all fluvial ecosystems, irrespective of their hydrologic regime.