The geological storage of nuclear waste includes multibarrier engineered systems where a large amount of cement-based material is used. Predicting the long term behaviour of cement is approached by reactive transport modelling, where some of the boundary conditions can be defined through studying natural cement analogues (e.g. at the Maqarin natural analogue site). At Maqarin, pyrometamorphism of clay biomicrites and siliceous chalks, caused by the in-situ combustion of organic matter, produced various clinker minerals. The interaction of infiltrating groundwater with these clinker phases resulted in a portlandite-buffered hyperalkaline leachate plume, which migrated into the adjacent biomicrite host rock, resulting in the precipitation of hydrated cement minerals.In this study, rock samples with different degrees of interaction with the hyperalkaline plume were investigated by various methods (mostly SEM-EDS). The observations have identified a paragenetic sequence of hydrous cement minerals, and reveal how the fractures and porosity in the biomicrite have become sequentially filled. In the alkaline disturbed zone, C-A-S-H (an unstoichiometric gel of Ca, Al, Si and OH) is observed to fill the pores of the biomicrite wallrock, as a consequence of reaction with a high pH Ca-rich fluid circulating in fractures. Porosity profiles indicate that in some cases the pores of the rock adjacent to the fractures became tightly sealed, whereas in the veins some porosity is preserved. Later pulses of sulphate-rich groundwater precipitated ettringite and occasionally thaumasite in the veins, whereas downstream in the lower pH distal regions of the hyperalkaline plume, zeolite was precipitated.Comparing our observations with the reactive transport modelling results reveals two major discrepancies: firstly, the models predict that ettringite is precipitated before C-A-S-H, whereas the C-A-S-H is observed as the earlier phase in Maqarin; and, secondly, the models predict that ettringite acts as the principal pore-filling phase in contrast to the C-A-S-H observed in the natural system. These discrepancies are related to the fact that our data were not available at the time the modelling studies were performed. However, all models succeeded in reproducing the porosity reduction observed at the fracture–rock interface in the natural analogue system.