In 2008, three short sedimentary cores were collected from Nanyihu Lake in the lower Yangtze River Basin using a gravity corer. Heavy metals, including Pb, Cu, Zn, Cr, Ni, Mn, and major elements, including Al, Fe, K, Na, Mg and Ti, were measured. Radionuclides, including 210Pb and 137Cs, were analyzed to date the sediments. The significant Mn enrichment in the uppermost sediments of the three cores did not influence the distribution of Pb, Cu, Zn, Cr and Ni. The Pb, Cu, Zn, Cr and Ni contents have increased over the past 30–40 years. The decline of 206Pb/207Pb ratios toward the surface indicated increasing anthropogenic Pb loading to the lake sediments. However, the heavy metal enrichment was low overall because of the high sediment accumulation rates and the low anthropogenic heavy metal flux into the Nanyihu Lake.