This study describes a straightforward fluorescence-based method using carbon dots (CDs) with a green chemistry synthesis process for the detection of the hazardous compound trinitrophenol and antibiotic ciprofloxacin, and electrochemical detection of flavonoid morin. CDs with an average size of 2.86 nm were synthesized via the hydrothermal method from green sources. The CDs act as turn “on–off–on” nanoswitches for the detection of trinitrophenol (TNP) and ciprofloxacin (CIP). The CD-based nanoprobe detects TNP via a fluorescence quenching mechanism. The limit of detection was determined to be 23.00 nM. CD–TNP complexes are then used as base probes for fluorescence enhancement to detect ciprofloxacin sequentially. The CD–TNP complexes were shown to have a detection limit of 32.90 nM for ciprofloxacin recognition. A combinatorial molecular logic gate that combines the logic operations NAND and NOT in a unique manner has been created to describe the turn “on–off–on” sensing. Also, a carbon dot-modified electrochemical sensor was fabricated for the selective and sensitive detection of morin with a lower detection limit of 14.20 pM. Furthermore, the application of this nanoprobe for sensing TNP and morin in real samples has been demonstrated. The findings of this work led to the creation of a novel sensing system that can serve as a foundation for the design of sensing probes for the detection of hazardous substances, chemical compounds, and flavonoids in biological applications.