The current study compares the tolerance, to Ni and Cu, of three species of phytoplankton, Urosolenia eriensis, Cosmarium minimum and Scenedesmus acutus, isolated from Alice Lake, Sudbury, Canada. An attempt was made to determine if metal tolerance is related to the presence and abundance of these species in the lake. Alice Lake was subjected to 60 years of Ni and Cu pollution from a nearby Ni–Cu smelter. After the closure in 1972, the air quality improved immediately and water quality began to improve by the late 1970s and early 1980s. Phytoplankton, which had been all but absent from the lake, had reappeared by the mid-1980s. Metal tolerance was measured in defined media allowing the computer modelling of speciation described as ‘free’ Ni and Cu. Nickel tolerance was compared with ambient lake water concentrations and the presence of each species. The order of tolerance for Ni was U. eriensis > C. minimum > S. acutus. All species had similar tolerance to Cu. Differences in tolerance alone did not explain the shifts in species dominance within Alice Lake. These results emphasize the difficulties with using laboratory trace-metal tolerance estimates to interpret ecological field observations.