Traditional Global Navigation Satellite System-Acoustic (GNSS-A) positioning assumes the Layered Model in the sound speed structure, and any of horizontal perturbation of seawater degrades its accuracy. However, the use of the Gradient Model analytically demonstrated that the horizontal gradient of the sound speed structure and displacement can simultaneously be solved using multiple transponders for each of ping. We applied this technique to our observed data and found it unsuitable for real data. We confirmed that a horizontal perturbation with wavelength shorter than the horizontal extent of the transponder array significantly violates the linear approximation in the Gradient Model. Our vertical 2D numerical simulation of internal waves (IWs) forced by tidal oscillation showed that such small-scale IWs could effectively be generated by nonlinear cascade from large-scale IWs of the major tidal constituents. In addition, a small-scale IW in deep water typically has a period of 3–4 h, which degrades positioning accuracy significantly, whereas an IW of much shorter period in shallow water has less effect after removal of the fluctuation by time averaging within a typical observation period. Apparent array position obtained in the synthetic test based on the simulated IW-derived sound speed structure showed features quite similar to that observed in real surveys. To incorporate such deeper perturbation, we proposed a Disturbance Model using dual sea surface platforms, that can solve time-varying perturbation in the vicinity of each transponder.