A three-dimensional model simulating the subsurface flow, microbial growth and degradation, microbial-chemical reaction, and transport of microbes and chemicals has been developed. The model is designed to solve the coupled flow and transport equations. Basically, the saturated-unsaturated flow field is described by the well-known Richards' equation with variant hydraulic conductivity changing with microbial and chemical concentrations. Seven components, namely one substrate, two electron acceptors, one nutrient, and three types of microbes, might exist in subsurface systems and compose seven simultaneous advective-dispersive-reactive transport equations. Since numerical problems may be introduced by using the conventional finite element method, the modified Lagrangian-Eulerian numerical scheme with adapted zooming and peak capturing is applied to solving these seven nonlinear partial differential equations accurately.