One of the main reasons for the surprising results that may be encountered in the construction of underground structures is that the rock masses have different formations. Deformations in the tunnel occur as a result of surcharge load from the structures on the surface, overloading, internal stresses in the rock or soil, and other factors. In-tunnel deformation measurement is important to determine the magnitude of plastic deformation in the tunnel and is an important step in monitoring tunnel safety. In this study, three-dimensional and non-linear behavior of tunnels designed as horseshoe or egg shape in a groundwater environment in a four-layered rock formation and gradually excavated with NATM (New Austrian Tunneling Method) principle were analyzed using the finite element method. The tunnel crown and wall, which were exposed to different loading conditions according to the excavation steps, were examined in detail in terms of permanent deformations. In addition, thanks to the deformation curves, the permanent deformations occurring along the critical sections of the tunnel during all excavation stages were compared relatively for both tunnel geometries. It has been determined that it is more advantageous to choose the tunnel geometry as egg-shaped rather than horseshoe type for reducing the settlement and the convergence in the shallow and layered rock environment.