A green and simple microwave-assisted method was used to synthesis water-soluble boron and nitrogen-co-doped carbon dots (B-N-CDs). These B-N-CDs were successfully used for the fluorescent determination of Sn and Mo ions. This probe had a fast response time at pH = 4 with high sensitivity and selectivity. Linear correlation between F/F and the concentration was seen in the range of 0.2-18 μM and 0.2-25 μM for Sn and Mo, respectively. Under optimum condition, the limit of detection (LOD) for Sn and Mo were 150 nM and 132 nM, respectively. The performance of the sensor was evaluated by different real samples such as tap, river and mineral water, canned fish sample and tomato samples.