Instream, overbank and cut riverbank exposures along the East Branch of the Finniss River downstream of Rum Jungle Mine, Northern Territory have been analysed for their total metal concentrations using instrumental neutron activation analysis (INAA). Concentration values for the < 62.5 μm and bulk sample fractions are compared to Australian sediment quality guidelines values (ANZECC/ARMCANZ, 2000). The results reveal that channel and overbank environments are contaminated with heavy metals, with many samples exceeding the low and high sediment guidelines values. The < 62.5 μm fraction is consistently more contaminated than bulk samples as are instream environments compared to adjacent overbank environments. Metal concentrations are strongly correlated to sediment pH and Fe values, suggesting that these variables are significant in controlling the spatial distribution of sediment-associated metals. The strong positive correlation between sediment-associated metals and Fe is probably related to the process of metal sequestration by Fe (and Mn) oxyhydroxides. The spatial distribution of sediment-associated metals downstream of the Rum Jungle Mine site does not display a simple distance–metal concentration decay pattern. It is suggested that the non-uniform spatial distribution of sediment-associated metals is a function of local, reach-scale variations in channel geometry and geomorphology, which control sediment storage and transfer patterns. In cut riverbank exposures the vertical of metals distribution is non-uniform and probably reflects differential metal mobility. Despite rehabilitation of the mine site in the 1980s, the elevated sediment-associated metal concentrations that remain within the East Branch of the Finniss River system are likely to render the system contaminated for the foreseeable future and limit the potential for the full recovery of aquatic and terrestrial flora and fauna.