This study presents the observations from a comprehensive Scanning Electron Microscopy (SEM) study of lime mortar from a heritage structure. Microstructural and geo-chemical characterization of carbonate, chloride and sulphate phases was performed based on Energy Dispersive Spectroscopy (EDS). The hydrated carbonates underwent polymorphic changes ranging between the vaterite, aragonite and calcite forms. The habit of crystallization of calcite widely varies depending upon its environment of crystallization amidst pore spaces and voids. The repeated influx and evaporation of capillary ground water and storm water into the lime mortar caused the precipitation of carbonate materials of wide compositional variation. The presence of halite mineral crystallized as interstitial skeletal or hopper crystals was found inside the mortars. Capillary channels filled with these crystals indicated that the capillary forces played a critical role in the influx and evaporation of pore fluids with successive chemical variations from bicarbonate ground water source contaminated with chloride ions. Presence of portlandite, anhydrite, and gypsum was confirmed along with minor traces of ettringite and thaumasite. Chemical compositions of these minerals indicated that they were crystallized from a common source of pore fluids of meteoric water composed with carbonates, chlorides and sulphates. The repeated differential order volume change by expansion and shrinkage had induced the development of hairline cracks and deformations in the lime mortar. © 2019 Elsevier Ltd