Photoexcited quantum dots (QDs) offer a wealth of mechanisms for interactions with the valence band holes or conduction band electrons, influencing electron–hole recombination. The potential to use combinations of these mechanistic pathways to achieve detection of different metal ions with one modified QD system has been tested. Dual-function water-soluble core/shell-modified CdSe/ZnS quantum dot nanoparticles have been created, that exploit two different fluorescence emission pathways for the detection of two heavy metal ions: Zn2+ and Mn2+. A QD-zincon system is proposed, which shows a static Perrin-type quenching mechanism, with sphere of action radii 1.1, 1.3 and 1.6 nm respectively, for 500, 540 and 620 nm QD emission. The QD-zincon system was produced using a layer-by-layer approach: mercaptopropionic acid-capped QDs were modified with a positive polyelectrolyte by electrostatic interaction and then a negatively charged chromogenic reagent, zincon, classically used for the determination of metals. QD-zincon is able to coordinate both Zn2+ and Mn2+ and, by exploiting two different mechanisms, QD-zincon conjugates can be tailored to respond to Zn2+ or Mn2+. Upon coordination of zincon with Mn2+, a dramatic enhancement of the fluorescence intensity results as the quenching interaction between zincon and QDs is deactivated, thereby ‘switching on the fluorescence emission’. The versatility of this system is demonstrated in terms of fluorescent emission wavelength, which could be selected across a wide range, through choice of QDs (examples are shown for λmax = 500, 540 and 620 nm). In contrast, in the case of Zn2+ detection, the mechanism is based on the radiationless resonance energy transfer (RET) from QDs acting as donor, to the acceptor zincon-Zn2+, since its absorption spectra offer adequate overlap with the emission spectra of QD540 and QD620, producing a useful analytical signal by the RET process. Using these different operating principles, CdSe/ZnS core/shell QD-zincon conjugates showed very good linearity in the range 10–1000 µM and 5–500 µM for Zn2+ and Mn2+ nanosensors, respectively, and RSDs about 3% (n = 10). In a study of interferences, the QD–zincon conjugate showed higher selectivity than the corresponding method with zincon in solution. The results from synthetic ionic mixtures suggested very good applicability in the determination of Zn2+ and Mn2+ in samples containing other metal ions, with just a small reduction of sensitivity at very high ionic concentration.