A great deal of progress has been made in recent years to investigate the chemical characteristics of beachrocks. Beachrocks found in Krakal-Sadranan Beach (Yogyakarta, Indonesia) are spread locally, parallel to the coastline with a breadth of about 10–30 m2. In this research, unmanned aerial vehicle (UAV) drone mapping, geological analysis, direct current resistivity survey, and surface seismic surveys were conducted to detect the underground structure of the beachrocks and to emphasize the coastal mapping based on targeted beachrocks. The correlation was developed between the sections and the data on the study site. Toward survey validation, laboratory tests were conducted on the beachrock samples collected from the study site to identify its properties. The evolution of the coastal zone based on beachrocks study is highly affected by relative sea-level changes that were described in the 3D model of beachrocks. The coastal changes are significantly impacting the natural and cultural resources, and the understanding of coastal evolution is important for the preservation, development, and management of the coastal zone. This paper focused on the cementation processes and mechanism of beachrocks as a natural wave barrier in a tropical area, which is also appropriate for advanced marine ecosystems study including shorelines microbiotas.