The marine site investigation is a key factor for the correct development of any project that must be conducted offshore. There is a wide range of tools designed to get information of the seabed in case of soil, either in-situ tests or sampling. Nevertheless, in the case of a rocky seabed, the options are limited. Drilling vessels with heave compensation are available and are especially useful for deep-sea waters and large investigation depths. For nearshore projects, the use of jack-ups with onshore drilling equipment on board is also common but limited to the maximum length of the spuds. However, the cost of mobilization of both systems is the main item in any geotechnical investigation and might be economically prohibitive. Therefore, there is a lack of a cost-effective system for shallow water projects when short target penetrations are required. The submersible drilling rig presented in this paper was designed and constructed with the aim to allow conducting investigations in a more effective way obtaining high-quality samples for soil or rock characterization. The system is instrumented with sensing elements allowing the full control of the test in real-time for three different purposes: (i) positioning, (ii) continuous drilling parameters, and (iii) visual inspection. The suitability in sandy and silty soils was reported by Romero et al. (2012). The system has outstanding as an interesting alternative to traditional methodologies for rock investigations in relatively shallow water projects where the knowledge of the first meters of rock profile is critical (pipelines, submarine interconnections, dredging, foundations). Some benefits of the system are presented in this paper, especially in ground models composed of a rock layer underneath a soil deposit or by rocks with variable strength with depth.