The Aral Sea has received worldwide attention for the deterioration of its biological and chemical status. The accumulation of potentially toxic elements (PTEs) in the lake sediments reflects changes in the surrounding watershed and represents a potential hazard for the lake ecosystem. In conjunction with existing environmental records from the Aral Sea basin, sedimentary records of PTEs in North Aral Sea covering a short time scale, anno Domini (AD) 1950–2018, were used to reveal historical changes in PTE concentrations and potential risks to lake functioning. The results suggested that the levels of PTEs in lake sediments from North Aral Sea changed abruptly around 1970 AD, which is concurrent with the intensification of human activities within the basin. After 1970 AD, with the exception of As, which remained at unpolluted-to-moderately polluted levels, the geo-accumulation indices of the remaining PTEs studied (V, Cr, Zn, Co, Pb, Ni, Cu and Cd) inferred a moderately polluted status. Before 1970 AD, the total ecological risk was low, but since 1970, the total ecological risk index has exceeded 150, indicating moderate risk. Historical changes in PTE levels of lake sediments from North Aral Sea and their potential ecological risks are reported for the first time. The conclusions provide an important reference for the protection of lake ecosystems and will provide data for regional/global comparisons of environmental change during the Anthropocene.