Windermere Arm is a 50-ha narrow channel located in the south-eastern portion of Hamilton Harbour, which is designated by the International Joint Commission (IJC) as one of the primary Areas of Concern in the Canadian waters of the Great Lakes. Sediments within the Arm have historically been contaminated with metals, PAHs, and to a lesser extent, PCBs. Sedimentological, geotechnical and geochemical investigations have been undertaken to determine the degree and the spatial extent of contamination. The thickness of contaminated sediment and their degree of contamination vary widely within the study site. Information on the thickness of contamination obtained from logging and chemical analysis of sediment cores agrees in general with the results of in situ penetrometer testing. Concentrations of Zn and Pb in some sub-samples are above the Severe Effect Level (SEL) for benthos set by the Ontario sediment quality guidelines. On average, surficial sediments tend to have lower metal concentrations than deeper sediments, probably due to the reduction of industrial point discharges. Apart from the two main boat slips, concentrations of PAHs are relatively low and in agreement with previously reported values. In contrast, new results yield higher values of PCB concentrations than previously reported, and 21 sub-samples of surficial sediment analyzed yielded values greater than 1 μg/g. Results suggest that the majority of recent PCB loadings are entering the study site from nearshore industrial spills or dumping, despite the detection of trace amounts of PCBs in a nearby creek. Pronounced sediment disturbance noted in several cores suggests that more contaminated historical sediments are at risk of being disturbed and re-exposed to the water column.