Sediment-borne contamination in a watershed can be highly variable as a result of fluvial processes operating over a range of time scales. This study presents a detailed analysis of the distribution of one contaminant along an ephemeral stream after 55 years of sediment transport, deposition, and exchange by flash floods. Wastewater containing plutonium was discharged into the Pueblo Canyon watershed from 1945 until 1964, and plutonium concentrations in fluvial deposits vary over five orders of magnitude. These variations can be attributed to three primary factors: time since contaminant releases, particlesize sorting, and mixing of sediment from different sources. The highest concentrations occur in fine-grained sediment deposits near the source that date to the period of effluent releases, and concentrations are lower in younger deposits, in coarser-grained deposits, and in deposits farther downstream. The spatial distribution of plutonium is strongly affected by longitudinal variations in the size of sediment deposits of different age. A major aggradation-degradation cycle in the lower canyon overlapped with the period of active effluent releases, and a significant portion of the total plutonium inventory is contained within large coarse-grained deposits below fill terraces that post-date 1945. The spatial pattern of contamination is thus determined by the specific geomorphic history of the watershed, in addition to processes of mixing and sorting during transport that occur in all fluvial systems.