This study aimed to use a simple, low-cost and eco-friendly microwave-assisted method for the synthesis of carbon dots-based fluorescent sensor that can detect more one target analyte in aqueous media. Herein, we report the synthesis of carbon dots (CDs) from peels of an indigenous and abundant wild fruit called wild medlar (Vangueria infausta). Functional groups such as hydroxyl (–OH) and carbonyl (C=O) were revealed on the surface of the as-prepared carbon dots using Fourier transform infrared spectroscopy (FTIR). The as-prepared CDs exhibited an amorphous structure and a broad distribution of particle size with an average size of 10 nm. In addition, the as-prepared CDs demonstrated excellent hydrophilicity and intense blue photoluminescence under UV light at 365 nm. The water-soluble CDs were employed for the detection of Al3+ using a ‘turn on’ mechanism and Hg2+ using a ‘turn off’ mechanism. Addition of increasing concentration of Al3+ resulted in an increase in the fluorescence intensity of the as-prepared CDs while addition of increasing concentration of Hg2+ resulted in quenching of the fluorescence intensity of CDs. The lowest limit of detection (LOD) for Al3+ and Hg2+ ions in aqueous media was determined at 817 nM and 612 nM, respectively. Furthermore, the as-prepared CDs have excellent selectivity towards Al3+ and Hg2+ among other potential metal ion interferences. Practical application of the as-prepared CDs towards detection of Al3+ and Hg2+ in tap water revealed good recovery rates of 86.0% to 87.4% and 96.4% to 106.5%, respectively. Therefore, this work has demonstrated a potent strategy for potential application of this nanoprobe towards dual detection of Al3+ and Hg2+ in aqueous samples.