Systematic error is one of the major factors that affect positioning accuracy owing to the changeable and complex nature of seawater environments. Based on a Global Navigation Satellite System-acoustic intelligent buoys system, whose acoustic array consists of a series of surface buoys, a single-difference method for underwater dynamic positioning is proposed to eliminate systematic error. Positioning configuration optimisation was addressed using dilution of precision (DOP). A simulation of DOP proved that for the single-difference method, a radiation network with a centre-difference reference point was superior to a regular polygon network. The positioning experiment showed that the novel method could effectively eliminate systematic error, improving vertical positioning accuracy from a metre- to a decimetre scale.