Amine-rich carbon dots (NCDs) have become promising nano-aminocatalytic platforms in organic synthesis. These nanomaterials can be effectively produced through straightforward bottom-up approaches using inexpensive nitrogen-containing molecular precursors as a starting material. However, to date, there is still a limited understanding of how the molecular features of these precursors affect the catalytic activity of the resulting nanoparticles. In this article, we describe the production of a new family of NCDs, which use L-Arginine and different alkyl diamines as starting materials. The surface amines of all these NCDs were comprehensively characterized, thus allowing us to provide a correlation between the structural features of the nanoparticles and their catalytic performance with a selected amino-catalyzed organic transformation. Importantly, the most active nano-aminocatalysts, namely, NCDs-3, were then used as a basis for the formation of a wide variety of functionalized organic compounds in water under mild reaction conditions.