The underground developments are likely to deteriorate the water quality, which causes damage to the structure. The pollutant levels largely affect the aquifer properties and alter the characteristics of the water quality. Ferritin nanoparticle usage proves to be an effective technology for reducing the pollutant level of the salts, which are likely to affect the underground structure. The observation wells are selected around the underground Metro Rail Corridor, and the secondary observation wells are selected around the corridors. Ferritin is a common iron storage protein as a powder used in the selected wells identified in the path of underground metro rail corridors. Water sampling was done to assess the water quality in the laboratory. The water quality index plots for the two phases (1995-2008) and (2009-2014) using GIS explains the water quality scenario before and after the Ferritin treatment. The Ferritin treatment in water was very effective in reducing the pollutants level of Fluoride and sulphate salts which is likely to bring damage to the structure.