If the orientation of a seafloor electromagnetic (EM) instrument is unknown, it has to be estimated afterwards, relatively early in the processing. Here we present a method to estimate the horizontal and vertical orientation of seafloor electromagnetic receivers. Three component magnetic recordings of the naturally occurring magnetotelluric field are utilized to find the tilt, pitch, and azimuth angle relative to a given reference. Estimation of angles is controlled by minimum difference criteria. Precautionary measures are necessary to eliminate the subsurface response in the recordings of the EM field components. The proposed method is applied to synthetic and real data, demonstrating that even in difficult geologic settings, the simple characteristics of the incident natural EM field allow us to quickly estimate the orientation of the instruments.