This paper presents a vision-based underwater mapping system, which is demonstrated in an archaeological survey of the submerged ancient town of Pavlopetri. The snorkeler or diver operated system provides a low cost alternative to the use of an AUV or ROV in shallow waters. The system produces textured three-dimensional models, which contain significantly more information than traditional archaeological survey methods. The photo-realistic maps that are produced allow further archaeological research to be performed, without diving on a site during the restrictive time limitations of permits and field seasons. The hardware and software components of the mapping system and its method of operation are described, and initial results are presented and discussed.