Establishing a numerical model can be described as the representation of a conceptional model of a natural system using numerical algorithms, such as an aquifer or a system of interacting aquifers. In this chapter, we will distinguish between two groups: cold (non-geothermal) and geothermal aquifers. Numerical models can be used to simulate responses due to perturbations of the system in order to evaluate the dominating influences on the more complex real-world systems. Using the basic laws of physics and chemistry that govern groundwater flow, and solute and heat transport, the conceptual model is mathematically represented. The conceptual model considers all the information available on geological setting, geometrical properties, hydraulic parameters, solid phase properties, including homogeneity and isotropy, fluid properties, boundary condition, both sources and sinks of fluids, solutes and heat, and their spatial time-dependent distributions within the study area and its boundaries. The purpose of the numerical model is to solve the differential equations either at steady state conditions for the unperturbed system, or to model the behavior of the domain over time.