Modern stromatolites at Highborne Cay, Exuma, Bahamas are formed in a high energy environment, where turbulent mixing of the water column supplies the sand particles that are trapped and bound by microbial phototrophs. The photosynthetic communities consist of cyanobacteria within the surface fabric of the stromatolite, and surface eukaryotic microalgae (e.g. diatoms and chlorophytes). Due to the turbulent environment, stromatolites are often buried for periods of weeks or months as a result of sand wave movements. We investigated the tolerance of subsets of the photosynthetic communities in stromatolites to natural burial processes. Variable chlorophyll fluorescence was used to monitor PSII quantum efficiency and fluorescence kinetics during and after artificial and natural in situ burial. Excavated samples with an intact cyanobacterial community, but lacking surface microalgae, reactivated their quantum efficiency when exposed to both low light and oxygen. Reactivation, indicated by an increase in photochemical efficiency (ΔF/Fm), occurred after 7 to 9 d and 14 to 16 d of natural burial, although reactivation was slower with longer burial. Changes in fluorescence yields indicated that probable state transitions occurred, and we suggest that some form of oxygen dependent process(es) and light were in part responsible for the re-establishment of photochemistry. These processes effectively ‘kick start’ electron transport, and hence protect against photodamage induced by exposure to light after burial. In contrast to the prokaryotic cyanobacterial mats, mats with surface communities dominated by diatoms did not have high tolerance to burial. Two out of 3 samples of diatom mats failed to reactivate after 7 d of burial. The greater ability of cyanobacteria to survive week to month long periods of burial may be an important factor in accounting for the importance of these prokaryotes in stromatolite construction.