Abstract Essential climate variables (ECVs) are physical, chemical, or biological parameters supporting the characterization of the climate system. The oceanic ECVs temperature and salinity have been defined for the sea surface (upper 1 mm) and bulk water (upper 2 meters). Direct observation and sampling of the sea surface from ships and buoys is limited due to the potential loss of integrity of the sea surface and contamination by the research platform. The design, development, and operation of a research vehicle with autonomous capabilities based on commercially available components are described in this study. The autonomous operation and fully automated sampling enable high-resolution mapping of the sea surface microlayer (SML), i.e., the upper < 1mm layer, and near-surface layer (< 1.2 m). Sampling the SML is based on a rotating glass disk sampler. The autonomous surface vehicle HALOBATES has been equipped with multiple conductivity, temperature, and depth sensors (CTDs) in a flow-through system to measure both sea surface and bulk temperature and salinity. The performance of the autopilot under various scenarios is demonstrated. Typical anomalies of ECVs within the SML and near-surface layer are evident and forced by both atmospheric and oceanic processes. Data analyses reveal HALOBATES' ability to resolve thermohaline structure on different spatial and temporal scales, for example, small-scale freshwater lenses and thermohaline changes across oceanic fronts. The integration of an Acoustic Doppler Current Profiler supports the interpretation of thermohaline structures. HALOBATES is a platform with cutting-edge technology for understanding climate-related processes between the ocean and atmosphere and providing high-resolution sea surface data for validating satellite products of ECVs.