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Salt crystallisation is a principal deterioration factor of many stone monuments. In this study, samples of weathering products of two baroque monuments in Ljubljana, Slovenia (the Fountain of Three Carniolian Rivers and the side altar of the Church of St. James), as well as the limestone used in their construction (Lesno Brdo limestone) were investigated in order to ascertain the main mineral phases produced during the weathering process. A combination of micro-Raman spectroscopy and X-ray powder diffraction was successfully applied to identify micrometre-size minor components in the limestone and the weathering product phases. In addition to calcite and dolomite as the main components of the Lesno Brdo limestone, quartz, anatase, goethite, haematite and phyllosilicates were also determined as minor limestone minerals. The limestone was found to be extensively deteriorated in both outdoor and indoor environments in the studied historical monuments, showing flaking, subflorescence, efflorescences, crumbling and black and white crusts as a result of the deterioration phenomena. Among these weathering forms, efflorescences were found to be more complex in terms of mineral assemblage, where gypsum was associated to hexahydrite, pentahydrite, and nitre. In contrast to the efflorescences, the mineralogy of subflorescences as well as that of white and black crust from outdoor and indoor conditions was rather simple, composed of only gypsum. The results showed that gypsum also crystallised under the surface as subflorescence, which eventually led to the flaking and crumbling of the limestone.