Mercury (Hg), as a highly harmful environmental pollutant, poses severe ecological and health risks even at low concentrations. Accurate and sensitive methods for detecting Hg2+ ions in aquatic environments are highly needed. In this work, we developed a highly sensitive fluorescence sensor for Hg2+ detection with an integrated use of biosynthetic CdSe/CdS quantum dots (QDs) and liposome carrier signal amplification. To construct such a sensor, three single-stranded DNA probes were rationally designed based on the thymine-Hg2+-thymine (T-Hg2+-T) coordination chemical principles and by taking advantage of the biocompatibility and facile-modification properties of the biosynthetic QDs. Hg2+ could be determined in a range from 0.25 to 100 nM with a detection limit of 0.01 nM, which met the requirements of environmental sample detection. The sensor also exhibited a high selectivity for Hg2+ detection in the presence of other high-level metal ions. A satisfactory capacity of the sensor for detecting environmental samples including tap water, river water, and landfill leachate was also demonstrated. This work opens up a new application scenario for biosynthetic QDs and holds a great potential for environmental monitoring applications.