We demonstrate the ppt-level single-step selective monitoring of the presence of mercury ions (Hg²⁺) dissolved in environmental water by plasmon-enhanced vibrational spectroscopy. We combined a nanogap-optimized mid-infrared plasmonic structure with mercury-binding DNA aptamers to monitor in-situ the spectral evolution of the vibrational signal of the DNA induced by the mercury binding. Here, we adopted single-stranded thiolated 15-base DNA oligonucleotides that are immobilized on the Au surface and show strong specificity to Hg²⁺. The mercury-associated distinct signal is located apart from the biomolecule-associated broad signals and is selectively characterized. For example, with natural water from Lake Kasumigaura (Ibaraki Prefecture, Japan), direct detection of Hg²⁺ with a concentration as low as 37 ppt (37 × 10⁻¹⁰%) was readily demonstrated, indicating the high potential of this simple method for environmental and chemical sensing of metallic species in aqueous solution.