Soils from lacustrine zones are initially subjected to a sedimentation process, this stage continues with desiccation and consolidation in a partially saturated state. When the soils are highly compressible, this occurs simultaneously with soil cracking. This is the case of the "Sabana de Bogotá". This zone is a great depth lacustrine deposit (600 m approximately) with a surface composed of highly compressible organic clays. These soils are affected by desiccation caused by the atmosphere, vegetation and subsurface water extraction. This process comes together with crack generation that may reach 7 m depth and 20 cm wide. Soil surface desiccation is a complex phenomenon where mass and heat interchange with atmosphere has a fundamental importance. In particular, some main factors that influence this process are: solar radiation, wind speed, temperature, precipitation, evapotranspiration, etc. Most of existing numerical model simulations for water flow in partially saturated soils consider the ground surface as a boundary with characteristics independent from atmospheric variables. In this paper a numerical model developed specifically to simulate the interaction between atmosphere and soil is presented. This model is applied to the conditions of the "Sabana de Bogotá".