Stones and rock fragments are typically found within soil profiles across various landscapes. However, knowledge on, and understanding of, their impact on hydraulic functions and processes are still lacking. Specifically, the presence of stones within the soil profile may increase water storage and availability to vegetation and reduce plant mortality in drylands. However, physically-based testing of stones effect on soil water budget components is overlooked. Experiments under laboratory conditions from soil columns, with two volume content t levels and two sizes of stones, were carried out in this research. Our results reveal that stoniness reduces the duration of stage-1 evaporation (S1) and consequently the overall cumulative evaporation, proportionally to their volumetric content and to the initial soil water content. The effect of stone size on evaporation was minor during S1 but was more pronounced during stage-2 (S2) — when the evaporation front migrates downward — with smaller stones reducing evaporation more than the larger ones. A recent evaporation model, assuming that transient evaporation is a succession of steady state solutions, was applied to explain the 2-phases evaporation process in a stony profile. The model results indicate that apart from changing the effective porosity of the soil profile by replacing a soil volume by stones, stoniness affects mainly the hydraulic conductivity function but practically not the water retention curve. Stoniness induced an increase in the tortuosity-related parameters compared with those of the stone-free soil. This observation was strengthened by the fact that both measured and modelled data reveal that stoniness has not affected the downward movement of the water table level during drying. Although we tested two stone sizes only and further experiments are required for a broader understanding, we suggest that the outcoming insights may improve estimates of water budget components in stony soil profiles and their response to global climatic changes.