The paper presents the results and assessment of the properties and capabilities of new types of surface hydrophobic agents for the treatment of fresh and matured surfaces of concrete and other cement-bound layers. Hydrophobisation prevents the premature evaporation of water and thus plastic shrinkage, which inevitably leads to the formation of cracks in cement-based structures. The influence of the new type of hydrophobic agents, epoxy water-based (EWH) and acrylate (AH) containing solvent, on the physical and mechanical properties of the treated concrete samples was assessed, including the adhesion of hydrophobisation on the concrete surface layers. It was confirmed that surface hydrophobisation successfully prevents premature evaporation of water, and thus, plastic shrinkage (concrete treated with EWH_0.3 showed more than two times lower shrinkage than reference concrete). The concrete samples treated by hydrophobisation agents showed higher strength after 120 days (37.5 MPa) in comparison with untreated concrete (32.8 MPa). Different properties were recorded with different types of hydrophobisation agents, including compressive strength after 90 days (31.2 MPa with EWH_0.15, and 35.9 MPa with AH_0.15). Water absorption after 120 days was lowest with EWH_0.3 samples (3.77%), two times lower than AH_0.15 (6.98%). The layer of hydrophobisation agent EWH_0.3 was thicker than AH_0.15, leading to lower water absorption of treated concrete and higher resistance to defrosting chemicals—waste 8.5. g/m2 with EWH_0.3 in comparison to 35.7 g/m2 with AH_0.15. Furthermore, a difference in the hydrophobisation behaviour was shown with blocking of infiltration from the chemically aggressive environment into the concrete substrate. Deterioration of the surface concrete exposed to 10% HCl solution was worse with AH_0.15; but the concrete surface treated with AH_0.15 showed better resistance than the EWH treated surface, when exposed to 5% CH3COOH. Degradation of the hydrophobisation integrity and the loss of cohesion between the concrete and the surface treatment after exposure to acetic acid and hydrochloric acid was observed using scanning electron microscopy (SEM).