This dataset contains hydrographic and biogeochemical observations collected during an oceanographic survey in Madagascar using Conductivity–Temperature–Depth (CTD) profiling systems. A total of 84 successful CTD casts were conducted using a Sea-Bird SBE 911plus CTD system mounted on a 12-bottle rosette sampler. Of these, 63 casts included discrete water sampling for analysis of pH, total alkalinity, dissolved nutrients, chlorophyll-a, dissolved oxygen, and salinity. Sampling was conducted at predefined depths and targeted the fluorescence maximum following established CTD rosette protocols. In deep stations (>500 m), full water-column sampling was performed for sensor calibration and validation. Salinity and dissolved oxygen samples were analyzed using a Guildline 8410A Portasal salinometer and a Metrohm 916 Ti-Touch Winkler titration system, respectively. The dataset supports hydrographic characterization, biogeochemical analysis, and CTD sensor calibration.