The aim of this work is to model the adsorption process used for mercaptan and water removal from natural gas. Three fixed beds containing Zeolite molecular sieve type 13X, are used in this plant. In this operation, two beds are in process for adsorption purposes and the other one is regenerated simultaneously. This system is also operated under isothermal condition. In modeling of this process, rate of adsorption is approximated by linear driving force (LDF) expression, and the extended Langmuir isotherm is used to describe adsorption equilibrium. The set of partial differential equations of dynamic model is solved by Crank-Nicolson method. The effect of equations of state is also studied and the best equation fitting the industrial data is selected. Also, concentration profile is presented versus bed length at various times. The influences of pressure, inlet concentration and bed height on the breakthrough time are also investigated.