Environmental regionalisations are useful tools for spatial planning and are mostly performed at the global scale to define biogeochemical provinces from surface data or in the mesopelagic zone. However, these regionalisations often lack separations at scales relevant for conservation as they do not always consider regional patterns such as island effects or regional dynamic patterns. Our study aimed to overcome these limitations by defining coherent physical and biogeochemical regions within the Southern Indian Ocean (20°W-160°E; 30°S-60°S), considering both spatial and temporal dynamics of environmental parameters. For this purpose, two complementary approaches have been used: one focusing on surface environmental data, and the other considering space-time dimensions through their vertical profiles. The first classical method, based on multivariate analyses, allowed us to delineate regions latitudinally due to the existing temperature and oxygen concentration gradient and revealed regional patterns such as highly energetic regions or productive areas. The newly developed second approach used functional analyses and provided additional information, including subdivision in the Subtropical Zone dominated by mesopelagic patterns. This subdivision results from temperature differences. It separates longitudinally the subtropical region with warmer waters found in the western area, likely transported from lower latitudes by the Agulhas Return Current. Climate velocities of temperature (i.e. speed of isotherm drift) were also computed for both epipelagic and mesopelagic regions to investigate their potential shift due to climate change. This environmental regionalisation brings relevant information to understand the distribution of the pelagic diversity and abundance and highlights the importance of accounting for vertical structures in a context of climate change.