The research focused on the damage caused by photosynthetic organisms that colonise frescoes and, more generally, stone surfaces in Roman hypogea with illumination systems. Phototrophic microbial communities responsible of deterioration of valuable historical, cultural and artistic sites are characterised, and their photosynthetic activity measured as oxygen evolution in situ and in culture. Amperometric and potentiometric microelectrodes were assembled for non-destructive and less invasive measurements of pH, O₂, NH₄⁺, NO₃^-, K⁺, Ca²⁺, (PO₄)^3- in order to assess chemical variations in the substrate due to the microbial metabolism. Measurements were also performed, at controlled light and temperature conditions, in mixed cultures of cyanobacteria and microalgae that are involved in the deterioration processes. Ecophysiological experiments were carried out on isolated photosynthetic species in order to verify ion and acidic compound production and release. ESI and EELS methods were applied for the sub-cellular localisation of elements of interest (C, O, N, Ca, P, Fe, S) and in order to identify cell structures involved in subtraction, accumulation and release of element from and in the environment. Spectral composition and irradiances available for the photosynthetic activity in the hypogea under investigation were recorded, and chemical variations in the substrate (measured) that may be due to the microbial metabolism under various light conditions. Data on the ecophysiological condition and metabolic activity of phototrophs were correlated to the chemical parameters measured in the communities and within the substrate with the aim to assess the mechanism of the damage on stone surfaces, to select significant parameters for the quantification of biodeteriogenic activity and to evaluate their use in monitoring stone surfaces by means of a multiparametric instrument.