Detection of mercury ion (Hg2+) contamination is of utmost importance as it poses a major ecological problem, and its increased accumulation would affect the flora and fauna. Herein we report an instrument free colorimetric sensing of Hg2+ using bio-functionalized gold nanoparticle (A-GNP). Digital image scanner (DIS) is used in the detection of Hg2+ based on the change in RGB AVG (Red, Blue and Green) intensities of A-GNP solution upon the addition of different concentrations of Hg2+. The limit of detection (LOD) for naked eye detection was 5 nM, while the DIS system had a LOD of 3 ppt and the limit of quantification (LOQ) 3.68 aM. This concentration is very much lower as compared to the permissible limits prescribed by the USA-EPA. RGB changes for lower concentrations of Hg2+ undifferentiated to naked eye was monitored using our digital image scanometer (DIS) and were cross verified using UV–vis spectroscopy. The DIS system was employed for testing tap water as well as ground water and the results produced were satisfactory in nature. The proposed DIS system can be used for on spot detection of water samples and the analysis does not involve tedious procedures such as sample collection, processing and storage prior to detection using traditional methods. The DIS system is both sensitive and selective and is specific to the detection of mercury. Thus, our study provides a highly sensitive and cost effective system for mercury detection in rural areas where the access to sophisticated instruments is negligible.