We documented arroyo evolution at the tree, trench, and arroyo scales along the lower Rio Puerco and Chaco Wash in northern New Mexico, USA. We excavated 29 buried living woody plants and used burial signatures in their annual rings to date stratigraphy in four trenches across the arroyos. Then, we reconstructed the history of arroyo evolution by combining trench data with arroyo-scale information from aerial imagery, light detection and ranging (LiDAR), longitudinal profiles, and repeat surveys of cross sections. Burial signatures in annual rings of salt cedar and willow dated sedimentary beds greater than 30 cm thick with annual precision. Along both arroyos, incision occurred until the 1930s in association with extreme high flows, and subsequent filling involved vegetation development, channel narrowing, increased sinuosity, and finally vertical aggradation. A strongly depositional sediment transport regime interacted with floodplain shrubs to produce a characteristic narrow, trapezoidal channel. The 55 km study reach along the Rio Puerco demonstrated upstream progression of arroyo widening and filling, but not of arroyo incision, channel narrowing, or floodplain vegetation development. We conclude that the occurrence of upstream progression within large basins like the Rio Puerco makes precise synchrony across basins impossible. Arroyo wall retreat is now mostly limited to locations where meanders impinge on the arroyo wall, forming hairpin bends, for which entry to and exit from the wall are stationary. Average annual sediment storage within the Rio Puerco study reach between 1955 and 2005 was 4.8 × 105 t/yr, 16% of the average annual suspended sediment yield, and 24% of the long-term bedrock denudation rate. At this rate, the arroyo would fill in 310 yr.