Sudbury (Ontario, Canada) has a long mining history that has left the region with a distinctive legacy of environmental impacts. Several actions have been undertaken since the 1970s to rehabilitate this deteriorated environment, in both terrestrial and aquatic ecosystems. Despite a marked increase in environmental health, we show that the Junction Creek system remains under multiple stressors from present and past mining operations, and from urban-related pressures such as municipal wastewater treatment plants, golf courses and stormwater runoff. Water samples have elevated metal concentrations, with values reaching up to 1 mg·L−1 Ni, 40 μg·L−1 Zn, and 0.5 μg·L−1 Cd. The responses of diatoms to stressors were observed at the assemblage level (metal tolerant species, nutrient-loving species), and at the individual level through the presence of teratologies (abnormal diatom frustules). The cumulative criterion unit (CCU) approach was used as a proxy for metal toxicity to aquatic life and suggested elevated potential for toxicity at certain sites. Diatom teratologies were significantly less frequent at sites with CCU values <1, suggesting “background” metal concentrations as compared to sites with higher CCU values. The highest percentages of teratologies were observed at sites presenting multiple types of environmental pressures.