Carbon-based nanoparticles, or carbon dots (CDs), were synthesized and modified using various starting materials. The CDs were characterized using UV-Vis, fluorescence, IR, and NMR spectroscopy to consider their structural and functional properties. These adjustments were analyzed to determine the effects on stability and fluorescence for future applications as biological and chemical sensors. pH studies were performed, and it was noted that the wavelength of absorption and intensity of fluorescence was stable in, and well beyond, the physiological pH range. Additionally, CDs synthesized from different carbon sources containing thiol functional groups were studied and cross-linked with catechol, 2-butyne-1,4-diol (BDL), and phloroglucinol dihydrate (PGL). CDs made from mercaptosuccinic acid (MSA) were most stable in solution and showed strong absorption and fluorescent properties after synthesis and cross linking modification. Studies comparing the cross-linking behavior of MSA and citric acid carbon dots were also carried out.