Water affects the susceptibility of stone to alteration by facilitating physical, chemical and biological weathering. Stone properties determine water transport and retention, but it is also expected that biofilms and extracellular polymeric substances could alter the water–stone relationship. A lot of research on this subject has been carried out on soils, but the effect on stones is understudied. For this reason, three sedimentary building stones, Ernzen, Euville and Savonnières, each with a different pore size distribution, were biofouled with cyanobacteria. Their relationship with the stone material was investigated by optical and electron microscopy, and the effect of cyanobacterial biofilms on water transport and retention was studied. The results showed that the cyanobacteria primarily colonize the building stones on the outer surface and have a limited effect on the water transport properties. They slightly reduced the capillary coefficient and drying rate of the stones, but enhanced the water content in the stone and increased water vapour sorption. They induced (near) hydrophobic conditions, but had no measurable effect on the gas permeability and water vapour diffusion. Moreover, swelling and shrinkage of the biofilms were observed, which could potentially induce physical weathering. It is expected that these changes could influence other forms of weathering, such as freeze–thaw weathering and salt weathering.