A near-surface disposal facility for low level radioactive waste is designed to isolate the waste and retard radionuclide migration from the disposal facilities to the biosphere for hundreds of years. To ensure the safety of the disposal facility, soil improvement techniques are required in order to upgrade the mechanical properties of its capping layers. In the present study, an emerging bio-cementation technique involving indigenous urea-hydrolyzing bacteria was explored as a soil improvement method for Israel`s national radioactive waste disposal site. The site is situated at the Nuclear Research Centre Negev (NRCN) and receives radioactive waste from hospitals, research institutions, higher education facilities and industry. Here, we show evidence supporting that indigenous urea-hydrolyzing bacteria are naturally present in the sandy soil of the Rotem-Yamin plain of the north-eastern Negev Desert in Israel. These bacteria were stimulated to hydrolyze urea into ammonium and carbonate, and were then incubated in the presence of calcium ions to induce calcium carbonate (calcite) precipitation, which can serve as a soil stabilizing layer. Stimulation experiments demonstrated that urea hydrolysis is feasible in soil samples collected from different locations in the region. Different rates of urea hydrolysis were evident in soil samples exhibiting differences in chemical composition and particle size. In addition, the rate of hydrolysis can be controlled by adjusting the energy source concentrations in the stimulation media. Overall, our data demonstrate the feasibility of stimulating indigenous urea-hydrolyzing bacteria and inducing calcite precipitation in northeastern Negev desert soil. This technique could be applied to improve capping layers of near-surface radioactive disposal sites.