Apart from the most common H-1 and O-16 we have the sister isotopes: deuterium D and O-18 in water. Isotope fractionation (the change in its concentration) occurs in any thermodynamic reaction. The isotopic composition serves as a distinct mark for each water sample. To carry out the isotope analysis of pore water, which may be used to reveal the source of excessive water in building elements, firstly one has to extrude water from voids. For this we tested three different methods of retrieving water from the porous material: squeezing and evaporation - the direct methods, dilution - the indirect method. The influence of capillary suction on the hydrogen and oxygen isotopes abundance ratio was also analysed. Materials whose substantial part of voids are gel pores (cementitious materials) act as a membrane during isotope transport separating lighter from heavier isotopes and therefore cause the fractionation of isotopes. The results of performed experiments indicate that moisture transport (capillary suction) has an influence on the isotopic composition of water. Therefore the isotope analysis can be useful in the investigation of moisture behaviour of porous building materials.