Reactive transport modeling is an essential tool for the analysis of coupled physical, chemical, and biological processes in the Earth system, and help resolve many issues in Earth sciences. Models describing the interactions of competing processes at a range of spatial and time scales are critical for connecting the advanced capabilities for materials characterization at the atomic scale with the macroscopic behavior of the complex Earth system. The Biosphere 2 Landscape Evolution Observatory (LEO) consists of three large-scale landscapes constructed inside an environmentally controlled greenhouse facility, and its goal is to develop an understanding of how climate, rock and biota interact over time to influence hillslope structure formation and its feedback to the movement of water through the landscape. Here we use a coupled model, CATHY (a 3-dimensional, variably-saturated, coupled surface-subsurface flow code) and CrunchFlow (a multicomponent reactive flow and transport code capable of simulating changes in the physical structure of the hillslope as a result of incongruent weathering processes) as a tool to further our understanding of the governing processes and interactions in the controlled LEO and natural hillslope systems. This model provides an ability to further examine the interactions and feedbacks between geochemical systems and complex subsurface flow fields. We will present the modelling method and some results of mineral weathering and neo-phase precipitation during the first experiment at LEO.