The paper explores the possibility of covering the mortar with the lightweight aggregate by the nanopolymer silane and siloxane as surface hydrophobisation. The investigation involved the mortars with two types of hydrophobic agents diluted with water in a ratio of 1:4 and 1:8. Mortar wetting properties were determined by measuring the absorbability, water vapor diffusion, contact angle (CA) and surface free energy (SFE) of their structure. Surface micro-roughness and 2D topography were evaluated. Scanning electron microscopy (SEM) has shown the microstructure and distribution of pores in mortars. The reduction in absorbency after the first day of testing by 87% was shown. An improvement in frost resistance after 25 cycles by 97% and an 18-fold decrease in weight loss after the sulphate crystallization test were observed. The hydrophobic coating reduces the SFE of mortars and increases the CA. In the case of using silanes, a 9-fold increase CA was observed.