Carbon dots (CDs) display photophysical features that appear similar, if not identical, despite the variety of synthesis protocols used to obtain them. The unique design of CDs toward the desired properties requires an exhaustive understanding of the structure itself. This work offers a fundamental insight into the structure and formation of the carbon dots that allows distinguishing the existence of molecular fluorophore species. Remarkably, density functional theory calculations of the elucidated structures support the spontaneous formation of a compact network of molecular species. In addition, as a proof-of-principle, our work comprehensively studies the photoluminescence properties (i.e., concentration, pH and solvent dependencies), which pave the way for developing CD-based logic gate fluorescent sensors.