A homogenous method is proposed for rapid detection of Pb2+ and Hg2+ using gold nanoparticles conjugated with T,G-rich aptamer. In presence of target ions the modified gold nanoparticles aggregate resulting in change of the solution colour from pink (for scattered nanoparticles) to blue (for their aggregates). Besides, the amplification system for this assay was proposed. It is based on the addition of 2-mercaptoethanol and allows decrease the limit of detection to 120 ng/ml for lead and 500 ng/ml for mercury compared to 1 μg/ml and 4 μg/ml for the method without amplification. The developed method is rapid (duration 20 min for environmental water samples), selective toward Pb2+ and Hg2+ and precise. It has a potential for practical application for water quality control and environmental monitoring.