For the underwater localization, acoustic sensor systems are widely used due to greater penetration properties of acoustic signals in underwater environments. On the other hand, the good penetration property causes multipath and interference effects in structured environment too. To overcome this demerit, a localization method using the attenuation of electro-magnetic(EM) waves was proposed in several literatures, in which distance estimation and 2D-localization experiments show remarkable results. However, in 3D-localization application, the estimation difficulties increase due to the nonuniform (doughnut like) radiation pattern of an omni-directional antenna related to the depth direction. For solving this problem, we added a depth sensor for improving underwater 3D-localization with the EM wave method. A micro scale pressure sensor is located in the mobile node antenna, and the depth data from the pressure sensor is calibrated by the curve fitting algorithm. We adapted the depth(z) data to 3D EM wave pattern model for the error reduction of the localization. Finally, some experiments were executed for 3D localization with the fast calculation and less errors.