Stem cell niches are complex multi-signalling networks comprised of molecular cues and physical interactions, orchestrated by niche-resident cells and the extracellular factors they produce. The bone niche specifically houses haematopoietic stem cells (HSCs), a critical cell type responsible for producing all blood and immune cells throughout life. Currently, how niches facilitate an ideal environment with simultaneously coordinating both intrinsic and extrinsic cellular signals is unknown. Studies presented here identify the existence of unique extracellular vesicle (EV)-defined niches within the haematopoietic system of human individuals. Bridging studies using proteomic signatures, nanoparticle characterization at single-vesicle resolution and machine learning-based techniques reveal that EVs can be grouped by blood, bone marrow and trabeculae within a human individual. Stem cell assays demonstrate that these niche-defined EVs impart functional effects on stem cells/progenitors based on location within the haematopoietic system. Finally, using single-cell transcriptomic analyses, results identify for the first time how niche-sourced EVs differentially affect the most primitive human HSCs and progenitors. This study highlights the significance of nanoparticles on human immunity and blood production and provides evidence for a new role for EVs, namely the demarcation of distinct nano-niches within biological systems.