The paper presents the experimental studies on the effect of the water containing micro-nano bubbles of various gases on the physico-mechanical properties of lime-cement mortars. In total, 7 types of mortars were prepared: with water containing the micro-nano bubbles of O2, O3 or CO2 as 50% or 100% substitute of ordinary mixing water (tap water) and the reference mortar prepared using tap water. In order to determine the influence of water with micro-nano bubbles of gases, the consistency of fresh mortar and the physical properties of hardened mortar, i.e., specific and apparent density, total porosity, water absorption by weight and capillary absorption, were established. The mechanical strength of the considered mortars was studied as well by conducting the tests for flexural and compressive strengths following 14, 28 and 56 days. Reduced workability and capillary absorption were observed in the modified mortars within the range of 0.9–8.5%. The mortars indicated an increase in the flexural strength after 28 days ranging from 3.4% to 23.5% and improved compressive strength in 1.2–31%, in comparison to the reference mortar. The conducted studies indicated increased flexural and compressive strengths along with the share of micro-nano bubbles of gases in the mixing water.