Diatoms and geochemical stratigraphy were studied in sediment core samples collected from a heavily polluted urban lake (SE China) in order to track the history of eutrophication and heavy metal contamination. The sediment profile covered ca. 60 years (from ca. 1951 to 2011) based on 137Cs and Spheroidal carbonaceous particles (SCP) dating, and encompassed a period of rapid industrial development in this region. Diatoms experienced two visible shifts, including the replacement of benthic and epiphytic taxa by planktonic species (e.g., Cyclotella meneghiniana Kützing) in 1972, and the dominance of Cyclotella atomus Hustedt and Nitzschia palea (Kützing) W. Smith after 1999. Metals (i.e., Cd, Pb and Zn), total phosphorus, total nitrogen and total organic carbon all increased in the past 60 years. Redundancy analysis was used to correlate diatom with chemical change and explained 50.3–60% of total variation in diatom data for three periods (from 1951 to 1999, between 1951 and 2011 and from 1972 to 2011). The combined effects of nutrients and metals were the predominant factor, capturing 29.6–42.8% of the total variance. Nutrients alone accounted for little more variance than did metals alone for the first flora shift about 1972. The further shift after 1999 was more influenced by the sole effect of metals than that of nutrients. Increases in species (e.g., N. Palea) able to tolerate both nutrient-related and metal-related stressors were related to persistent nutrient and metal inputs. In addition, climate warming might exacerbate eutrophication and metal contamination in this lake.