In order to meet demands for crops, pasture and firewood, the rate of land use change from forested to agricultural uses steadily increased over several decades, resulting in an increased release of nutrients towards groundwater and surface water bodies. In parallel, the degradation of riparian zones has diminished their capacity to provide critical ecosystem functions, such as the ability to control and buffer nutrient cycles. In recent years, however, the key environmental importance of natural, healthy ecosystems has been progressively recognized and restoration of degraded lands towards their former natural state has become an area of active research worldwide. Land use changes and restoration practices are known to affect both soil nutrient dynamics and their transport to neighboring areas. To this end, in order to interpret field experiments and elucidate the different mechanisms taking place, numerical tools are beneficial. Microbial decomposition is the main driving force on biogeochemical transformations of soil organic matter and soil nutrients. The activity of the soil biota is primarily controlled by water availability and by the pore-solution oxygen concentrations, which ultimately depend to a large extent on meteorological conditions, e.g., precipitation. In this work a model is presented that simulates carbon and nitrogen turnover and transport in a 1D profile under variably-saturated conditions. The model is based on the mechanistic batch model of Porporato et al. (Adv. Water Res., 26: 45-58, 2003), but extends its capabilities to simulate the vertical transport of the mobile components. Furthermore, oxygen dynamics are included such that the pore-water concentration is dependent on microbial degradation rates and soil moisture level. The model was applied to simulate the effect of land use change from forested to agricultural soils on pedo-fauna activity and nutrient distribution and abundance across the vertical profile. External forcing, i.e., precipitation time series, were generated stochastically. Modeling results showed that soil tillage practices, which modify soil structure and thus soil aeration, were responsible for higher decomposition and mineralization rates in agricultural soils, thus for the lower soil carbon and nitrogen concentrations. Furthermore, higher plant uptake rates and leaching of agricultural soils contributed also to lower nitrate concentrations in such soils.