Between external position updates, the most useful technique for trajectory estimation of a submerged drifter is dead reckoning (DR). These devices drift with the water current to measure the current’s velocity or to observe physical phenomena. We focus on the specific but important case of when the drifter, due to its size and shape, experiences acceleration by the water current, an effect that must be taken into account during the DR. The force induced by the water current over the drifter is translated into a shift in the heading direction, thus creating a horizontal (sideslip) and a vertical (angle of attack) directional angles between the drifter’s moving direction and its body frame. In this paper, we extend and modify techniques used for pedestrian DR and propose PCA-DR: a principle component analysis-based DR algorithm to estimate the directional angles. Used for cases where the water current is significant such that its force induces acceleration over the drifter and used only for short time periods of a few seconds between navigation fixes, PCA-DR uses acceleration measurements only and does not assume knowledge of the drifter’s dynamics. Instead, as part of the DR process, PCA-DR estimates the directional angles induced by the water current. Compared to the traditional DR approach, our results demonstrate good navigation performance. A designated sea experiment demonstrates the applicability of PCA-DR in a realistic sea environment.