We compared contaminants in zebra and quagga mussels (Dreissena polymorpha and Dreissena bugensis) of two different size classes from sites within the Niagara River to determine if the two species and two size classes can be used to monitor contaminants. Composite samples (i.e., at least 50 individuals) were analysed for 7 trace metals, total PCBs, selected organochlorine pesticides, chlorinated benzenes, and dioxins and furans. ANOVAs and MANOVAs showed that metal tissue concentrations varied significantly among sites, species, and size classes (P < 0.05). At sites where metal concentrations differed between species, zebra mussels had higher concentrations than quagga mussels. Similarly, larger mussels (i.e., 16-25 mm) generally had higher tissue concentrations than smaller mussels (<15 mm length). However, differences in tissue concentrations between size classes were present only for Cd, Cu and Mn and were infrequent, making these results inconclusive. For organic contaminants ANCOVAs and MANCOVAs using lipid concentration as a covariate revealed significant differences in tissue concentrations between the three sites, whereas differences between size classes were modest (P = 0.035). The ANOVA using individual parameters did not show a significant difference in tissue concentrations between the two size classes. In general, mussel tissue concentrations among stations (up to 7 stations throughout the river), were similar for Pb, Zn, Hg and Ni using data separated by species and size class. Concentrations of Cu, Mn and Cd were variable throughout the upper and lower Niagara. Tissue concentrations of α-BHC, 1,2,3 and 1,2,4 trichlorobenzene were similar in quagga mussels collected from 8 stations from the Canadian and American side of the river, whereas concentrations of total PCBs, octachlorostyrene, 1,2,3,4-tetrachlorobenzene, pentachlorobenzene and hexachlorobenzene were higher in quagga mussels from the American side of the upper river.