On 12 December 1992, an earthquake, followed by a tsunami, occurred on Flores Islands, creating massive damage in the northern area and resulting in an early warning tsunami for the Labuan Bajo region. This area is a high-priority tourist designation in Indonesia with busy offshore activities and infrastructure development. Thus, earthquake and tsunami mitigation strategies are mandatory. Part of the mitigation effort is mapping the seafloor and characterizing oceanographic conditions in the deep-water north of this area. This paper describes the seafloor and oceanographic conditions using a multibeam echosounder (MBES) survey, conductivity-temperature-depth (CTD) measurement, and current observation. Results show that the rough and complex seafloor topography is revealed in the study area. Seafloor topography consists of a steep slope on the nearshore, flat topography in the sublittoral and shelf, a steeper slope in the bathyal zone, and relatively flat in the abyssal zone found from the south to north in the area. In addition, physical oceanographic properties are observed in two locations with a maximum depth measurement of 3,029 m. The result indicates that the water column is divided into three layers based on gradient changes: surface layer, thermocline layer, and colder depth layer. Moreover, two single-point current measurements at the exact locations are carried out at water depths of 3,029 m and 1,880 m. Result also describes that both stations have current directions of 128.14° and 124.49°, with current magnitudes of 0.1693 m/s and 0.3724 m/s, respectively. This investigation could serve as primary data and information in the study area. Furthermore, it could support the government and other stakeholders related to the development of Labuan Bajo, e.g., infrastructure (submarine cable, port, etc.) and resilience program (e.g., tsunami early warning system) that region