Nitrogen-doped carbon dots synthesized from citric acid as a carbon precursor have recently been considered to contain fluorescent derivatives of citrazinic acid, which contribute to their emission in the blue spectral range. To study the impact of such molecular fluorescent species on the optical properties of carbon dots, we synthesized three samples employing citric acid and three different nitrogen sources: ethylenediamine, hexamethylenetetramine, and triethanolamine. On the basis of the analysis of the nitrogen content and its coordination by X-ray photoelectron spectroscopy, FTIR spectra, and systematically comparing absorption, steady-state emission, and photoluminescence decays of each kind of carbon dot, we derive the influence of the molecular precursors and gain further understanding of the complex structure of carbon dots highlighting the strong impact of molecular fluorescence in the samples produced with ethylenediamine and hexamethylenetetramine.