Despite known historical release of polybrominated biphenyls (PBBs; brominated flame retardants) into the Pine River (St. Louis, MI, USA), a tributary of the Tittabawassee River which subsequently forms the Saginaw River and flows into Saginaw Bay-Lake Huron, little is known about spatial patterns of sediment contamination by PBBs in this watershed. In this study, concentrations of two groups of brominated flame retardants, polybrominated diphenyl ethers (∑PBDE; BDE-28, -47, -66, -100, -99, -85, -154, -153, -138, and -209) and PBBs were measured in more than 120 floodplain soil samples, surface sediment samples, and sediment cores collected in 2004 from the Shiawassee River, the Saginaw River, and Saginaw Bay, Michigan. In addition, sediment samples collected in 2002 from the Pine River and the Tittabawassee River were analyzed, to elucidate riverine transport and attenuation of PBBs and PBDEs in this watershed. The mean concentration of ∑PBDE decreased from upstream to downstream, from the Shiawassee River and the Tittabawassee River to Saginaw Bay. BDE-209 was the predominant congener, accounting for 79% of the total PBDE concentration in the Shiawassee River and 90% in the Saginaw River. BDE-209 was followed, in order of decreasing abundance, by BDE-47, -99, and -100. The proportions of BDE congeners varied by water body, and by sample type, whether floodplain soil or sediment. High ∑PBDE concentrations were found in floodplain soil collected from the Shiawassee River near Chase Lake (55 ng/g, dry weight) and in sediment from the Saginaw River near Middleground Island (49 ng/g, dry weight). There was a significant positive correlation between ∑9PBDE (tri- to hexa-BDE) and BDE-209 in samples collected from the Shiawassee River and Saginaw Bay, but not in samples from the Saginaw River. Among PBBs, bromobiphenyl congener 153 (BB-153) was found in sediments from the Saginaw River but not in sediments from the Shiawassee River. An elevated concentration of BB-153 (13.5 ng/g, dry weight) was found in floodplain soil collected from the Pine River. The BB-153 concentration in sediment decreased by two to three orders of magnitude, from the Pine River downstream to Saginaw Bay. An elevated concentration of BB-153 (4.7 ng/g) was found in sediment collected from the mouth of the Saginaw River. Surface sediments collected near the mouth of the Saginaw River contained higher concentrations of both PBDEs and PBBs than did the subsurface sediments at these locations.