The widespread pollution of fluoride ions in the environment badly affects the ecological system due to their high toxicity, mobility and the difficulty of their degradation. So, there is a need to design an environmentally friendly, highly selective and sensitive probe for their detection. Here, we have used natural ingredients (e.g. mosambi peels (Citrus limetta), L-ascorbic acid and urea) and mild reaction conditions to synthesize oxygen and nitrogen-rich fluorescent C-dots, named as OC-dots and NC-dots, respectively. We have proposed a turn-off/-on strategy for the specific recognition and quantification of F⁻ ions. Initially, based on the fluorescence resonance energy transfer (FRET) mechanism, the selectivities of both types of C-dots were investigated towards ten different cations. Both types of C-dot were found to be selective for only Fe³⁺. The sensitivity of the OC-dot/NC-dot–Fe³⁺ system was also evaluated for fluoride ion detection and it was found that the OC-dot–Fe³⁺ ion mixture was only selective for F⁻ ions. The detection limit of the nanoprobe was found to be 0.01 μM, lower than the fluoride toxicity level defined by the U.S. Environmental Protection Agency (>1.5 ppm). The efficiency of the nanoprobe was compared using inductively coupled plasma atomic emission spectroscopy on real samples. The C-dot sensors were operated as different logic gates at the molecular level. All of the experimental data indicated that this probe is green, economical, quick and selective and can be used for establishing chemical logic gates for the detection of F⁻.