Metal pollution in water sources due to modernization is a human health and environmental problem. Therefore, the highly fluorescent boron- and nitrogen-doped and nitrogen-doped carbon quantum dots (B,N-CQDs and N-CQDs, respectively) were synthesized and investigated to be used as a fluorescence sensor for metal ion detection. In this study, the synthesized B,N-CQDs and N-CQDs had an average size of 4–6 nm and 3–4 nm, respectively. The B,N-CQDs presented high sensitivity as 0.0090, 0.0086 and 0.0091 units per micromolar for Cr3+, Cu2+ and Fe2+, respectively, whereas the N-CQDs showed sensitivity as 0.0047, 0.0102, 0.0095 and 0.0121 units per micromolar for Cr3+, Cu2+, Fe2+ and Ni2+, respectively. In the concentration range of 10–80 μM, the detection limits of B,N-CQDs and N-CQDs were found to be in the range of 13.9–65.5 μg/L and 14.9–38.3 μg/L, respectively. The result of the study clearly indicates that B,N-CQDs and N-CQDs can be seen as metal ion sensing devices with high sensitivity and low cost.