In this work, we aimed to tune the aggregation state of Au colloids by judicious regulation of their surface charges and by introduction of ultrasound irradiation. Au colloids were prepared by reduction of HAuCl4 with NaBH4 in the presence of 3-mercaptopropionic acid (MPA) as the stabilizing ligand. The Au colloids capped with MPA molecules possessing a single -SH terminal group, can form either linear or spherical Au colloid aggregates depending on the MPA Au ratio, solution pH and Au colloid concentration. Adjustment of these parameters provides a convenient means of regulating surface charge on the Au colloid surface and, thus, the state and degree of aggregation. The spherical aggregates appeared to be thermodynamically stable, and ultrasound irradiation could promote their formation. Intense ultrasound irradiation resulted in the formation of well-crystallized nanospheres whilst mild irradiation tended to produce a more amorphous product. This is the first observation of a sonication effect on the crystallization state in freely suspended Au colloids in aqueous solution.