Longitudinal patterns in the cadmium and mercury content of burrowing mayflies (Hexagenia) and surrounding sediments were examined along a 572-km reach of the upper Mississippi River. Surficial sediments and Hexagenia nymphs were sampled in 1989 at 12 sites extending from Pool 2 through Pool 16 and analyzed for total recoverable cadmium and total mercury. In sediment and nymphs, concentrations of both metals were highest in Pools 2, 3, and 4, which are just downstream from the Twin Cities (Minneapolis-St. Paul, Minnesota) metropolitan area, the primary anthropogenic source of metals to the studied reach of river. Concentrations of the two metals in sediments indicated a significant anthropogenic contribution, which was most pronounced for cadmium. The cadmium concentrations in surficial sediment varied less than 3-fold (range, 1.19–3.23 μg/g dry weight) among the 12 sites, whereas concentrations in Hexagenia varied almost 20-fold (range, 0.13–2.35 μg/g dry weight). Nymphs from Pools 2–4 had much greater concentrations of cadmium than nymphs from sites further downstream, even though the mean concentration of cadmium in sediment from Pools 2–4 (3.0 μg/g) was just twice that (1.6 μg/g) for the nine sites downstream. Mercury in sediments from the 12 sites ranged from 0.038 to 0.165 μg/g dry weight, averaging 0.14 μg/g in Pools 2–4 and 0.056 μg/g in the nine sites downstream. In nymphs, mercury concentrations ranged from 0.041 to 0.134 μg/g dry weight. The bioavailability of sediment-associated cadmium seemed greater in Pools 2, 3, and 4 than in the sites further downstream, based on the relative cadmium concentrations in Hexagenia nymphs and sediment. Moreover, it is concluded that the trapping of sediment and associated metals in Lake Pepin (a natural riverine lake in Pool 4) significantly reduces the exposure of the ecosystem further downstream to metals from the Twin Cities and other upstream anthropogenic sources.