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The diagenetic history of calcareous fossils is required for their application as palaeoenvironmental indicators. In this study, cathodoluminescence-microscopy (CL microscopy) and back scatter electron image–energy dispersive X-ray spectroscopy (BSE–EDS microscopy) were applied to Pliocene rhodoliths from the Azores Archipelago (NE Atlantic) in order to gain additional insight regarding the trace element content distribution throughout the algae thalli, and to ascertain palaeoenvironmental interpretations. Two types of luminescence were obtained: (1) high and (2) low luminescence. Rhodoliths with high luminescence are related with high concentrations of Mn 2+ in seawater and low luminescence rhodoliths are related with low concentrations of Mn 2+ in seawater. When the rhodoliths were deposited at about 4.0–4.5 Ma, the shoreline configuration of Santa Maria Island was much different than today. The influence of volcanic activity due to the extrusion of lavas and associated products and/or the presence of active shallow-water hydrothermal vents, was reflected in the sea water chemistry, with penecontemporaneous palaeoshores of the island featuring a high sea water concentration of Mn 2+ , which mirrored on the rhodolith Mn 2+ high concentration. By contrast, rhodoliths located about 2.8 and 2.9 km from the shore, in areas with low seawater Mn 2+ concentration, had low luminescence, reflecting the low Mn 2+ concentration in seawater. Rhodoliths chemical data and the geological history of the island proved to be congruent with the palaeogeographical reconstruction of Santa Maria Island at the time of the formation of the rhodoliths. [ABSTRACT FROM AUTHOR]