Mineral building materials are porous materials. The volume of pores connected is the active volume of pores or the effective volume. The volume of all pores is the total volume of the pores. The properties of the individual pores are different. Their dimensions and shape can influence the properties of materials. Materials are modified with different admixtures to improve their properties. However, additives or admixtures can cause corrosion. Although building materials do not provide food for microorganisms, they are very often inhabited by them. As a result of their presence and the action of metabolic products, biodeterioration occurs. One of the products of metabolism is water. In this paper we investigated how the modified structure of biodeterioration caused by mould fungi affects the moisture content of cement-polymer mortar with the admixture of polysiloxane latex.