Mercury exposure constitutes an acute risk to human health and the environment. Driven by the requirement to monitor trace-level mercury, we report a highly sensitive mercury(II) DNA sensor enhanced by silver(I) activation, followed by mercury(II)-specific oligonucleotides (MSO) molecular configuration switch and mercury(II)-modulated FRET. Activating the MSO strands with silver(I), mismatched cytosine–silver(I)–cytosine bridges induce individual MSO strands to fold readily in response to mercury(II) resulting in enhanced fluorescence signal. The structural switches were studied by 2D 1H–1H NOESY and TOCSY NMR spectroscopy, and 260 nm absorbance. The signal decreases with increasing mercury(II) concentration from 100 pM to 0.1 mM. The approach affords outstanding mercury(II) selectivity over other environmentally associated metals. Furthermore, the methodology was deployed for detection of mercury(II) in spiked pond waters with 97.9–100.6% recovery. The simple and feasible format has great potential for developing a cost effective and useful tool for environmental monitoring.