Up until the last ten years, remote sensing data and especially high-resolution satellite data and airphotos were mainly used in shallow water mapping. The evolution and low cost of unmanned aerial vehicles (UAVs) provides a new tool for coastal area monitoring. This paper presents the synergistic use of a small commercial UAV and an unmanned surface vehicle (USV) for beachrock mapping in Syros Island, Greece. RGB images collected with a quadcopter were processed using Structure from Motion (SFM) photogrammetry in order to create digital surface models (DSMs) and orthophotos of the coastline. A beachrock lying in shallow waters was detected and mapped using the UAV derived products. At the same time, a USV equipped with a compact side scan sonar (SSS) and bathymetric sonar system, provided the shape of the beachrock by mosaicking the backscatter strength of the SSS. In order to evaluate the results of the UAV and USV data derivatives, the beachrock perimeter and its depth were also mapped using a differential global navigation satellite system (GNSS) receiver. During the fieldwork, samples from the beachrock were collected and analyzed in the laboratory. The mineralogical composition of the bulk samples was determined by powder X-ray diffraction (XRD). Further petrographic study was also performed by petrographic polarizing microscope, macroscope, and scanning electron microscopy (SEM). Beachrock samples are classified as fine to medium grain sandstones and conglomerates. The mineral compositions of their grains and lithoclasts reflect the bedrocks of Syros Island (mainly metamorphic rocks) while a micritic high-Mg calcite constitutes the cement of these rocks.