The position of a seafloor geodetic station can be determined by combining Global Navigation Satellite System (GNSS) and acoustic technologies, called GNSS-acoustic positioning. The precision of GNSS-acoustic positioning, a technique that employs the distance intersection, is determined by the positioning geometry formed by the ship’s track lines with respect to the seafloor station and the errors in the measurements. In the context of a shallow sea trial, we studied three key techniques in GNSS-acoustic positioning: the optimal geometric configuration, differencing techniques for acoustic observations and depth constraints offered by pressure gauges. The results showed that the optimal geometric configuration is a circular track with a radius of $$ \sqrt 2 $$ times the depth plus an overhead cross-track with a length of the circle diameter. Differenced observations can improve the horizontal positioning precision but will worsen the vertical positioning precision due to the change in the geometric configuration and the elimination of vertical information if the number of observations is limited. The proposed difference strategy, that is, applying a symmetric location difference operator to the circular track and an undifference operator to the cross-track, can effectively improve the horizontal precision and avoid vertical defects. By using relative depth observations from two pressure gauges as constraints, the vertical defects of GNSS-acoustic positioning can be improved, achieving a better vertical positioning precision. Applying the proposed methods to high-quality GNSS and acoustic observations, the positioning precision of a shallow seafloor geodetic station can be better than 2 cm.