Although numerous methods have been reported for the analysis of toxic mercury (Hg2+) ions in drinking water, development of simple, rapid, inexpensive, and sensitive sensors still remains a great challenge. Here, we report a simple yet very sensitive colorimetric assay for rapid detection of Hg2+ in water. The colorimetric assay is based on the aggregation of as-prepared citrate-capped gold nanoparticles (AuNPs) in the presence of He ions and the positively charged amino acid, lysine. The detection limit of this inexpensive colorimetric assay is 2.9 nM, which is below the limit value (10 nM) defined by the U.S. Environmental Protection Agency in drinkable water. Also, the colorimetric response of citrate-capped AuNPs in the presence of lysine is very selective to the Hg2+. In addition, the colorimetric assay is very fast, and all analyses can be completed within a few minutes.