Herein, a facile hydrothermal treatment of lime juice to prepare biocompatible nitrogen-doped carbon quantum dots (N-CQDs) in the presence of ammonium bicarbonate as a nitrogen source has been presented. The resulting N-CQDs exhibited excitation and pH independent emission behavior; with the quantum yield (QY) up to 40%, which was several times greater than the corresponding value for CQDs with no added nitrogen source. The N-CQDs were applied as a fluorescent probe for the sensitive and selective detection of Hg(2+) ions with a detection limit of 14 nM. Moreover, the cellular uptake and cytotoxicity of N-CQDs at different concentration ranges from 0.0 to 0.8 mg/ml were investigated by using PC12 cells as a model system. Response surface methodology was used for optimization and systematic investigation of the main variables that influence the QY, including reaction time, reaction temperature, and ammonium bicarbonate weight.