The lower 9 km of the Buffalo River that flows into the eastern end of Lake Erie has been designated by the International Joint Commission as a Great Lakes area of concern (AoC) because of poor water quality, degraded riparian and river habitat, and contaminated sediments—impairments related to a long history of contamination from the industrial legacy of the past century. As a designated AoC, attention is presently focused on sediment remediation, an endeavor requiring an assessment of the relationship between sediment transport processes and sediment contaminant concentrations. In 1990 a pilot sediment trend analysis (STA) revealed an upriver return of sediments from the mouth of the Buffalo River as far as 5 km inland. A complete STA conducted in 2004 confirmed the upriver transport regime. Examination of river discharge and Lake Erie water levels demonstrated that lake seiches occur at far greater frequencies than river discharges of a magnitude capable of transporting sediment. Thus the river is behaving in a similar manner to an estuary with seiche rather than tidal waves responsible for driving fine-grained sediments in an inland direction. The dynamic behavior of the sediments as determined by STA correlated well with the expected contaminant levels contained in the sediments of the main river channel. The findings are used to establish a conceptual understanding of the river that requires extreme river flows to transport sediments to its mouth, after which sediments recently deposited from plumes discharging into Lake Erie are reentrained and transported upriver by seiche activity. Such an understanding is of considerable importance in sediment remediation as contaminants are also in a constant state of recycling both up and down the lower 5 km of the Buffalo River.