Cottonwood/willow forests in the American Southwest consist of discrete, even-aged vegetation patches arranged in narrow strips along active and abandoned stream channels of alluvial flood plains. We used the heat-pulse velocity technique in this study to estimate transpiration in 12 such forest patches along a perennially flowing reach of the San Pedro River in southeastern Arizona, USA during five periods from April to October 1997. Transpiration per unit sapwood area was consistently higher for the larger cottonwood trees found on outer secondary channels compared to that of smaller cottonwood trees along the active channel, but statistically significant differences were found only in August and October. Conversely, transpiration per unit sapwood area in willow was markedly higher for trees along the primary channel than for those few larger trees that were sampled on the outer margins of the forest. Average daily transpiration at the canopy scale among the patches in July was 4.8±0.7mm per day and ranged from 5.7±0.6mm per day in young forest patches adjacent to the primary stream channel to 3.1±0.6mm per day in more successionally advanced patches on secondary channels. Differences in our estimates of transpiration between forest patches along primary and secondary stream channels were related to differences in the ratio of sapwood area to ground area of the forest patches, and leaf area index. Estimates of transpiration from this forest type, and projections of transpiration and groundwater flux over larger areas on the San Pedro River, should take into account structural variation in these forests that relate to population dynamics of dominant trees.