Periphyton was collected on navigational buoys in the Montreal island sector of the St. Lawrence River during 1994–95 to compare biomass and species composition in the transparent “green” waters originating from the Great Lakes with those found in the colored, more turbid “brown” waters coming from the Ottawa River. Periphyton biomass (chlorophyll a, ash free dry mass, density and biovolume) was depressed in brown waters and differences in species composition were observed at the class (i.e., diatoms more important in brown waters) and species level (i.e., Melosira varians more abundant in brown waters). Comparison of 1994 and 1995 with 1982 and 1973 data supported the observed differences in biomass between brown and green waters, yet showed no major temporal shifts in periphyton species composition despite reductions in phosphorus loadings to the Great Lakes and the St. Lawrence River during that 20-yr period. Biomass (density and biovolume) of Cladophora and relative abundance of chlorophytes appeared much higher in 1982 than recorded in 1994 and 1995. Cladophora influences diatom community composition by providing a substratum for epiphytes and thus represents a key species controlling the structure of periphyton assemblages. Future monitoring efforts in the St. Lawrence River should focus on this species and include a standardization of sampling and enumeration methods.