Perchlorate ions (ClO4−) are prevalent contaminants in the surface, and drinking water that disrupt thyroid function by competitively inhibiting the sodium-iodide symporter (NIS), posing significant health risks. Here, fluorescence-based logic gates have been constructed by leveraging the binding interactions between a hemicyanine dye, 4-[4-(dimethylamino)-styryl]-1-docosylpyridinium bromide (DASPC22) and β-cyclodextrin (β-CD) that could be useful to know whether ClO4− ions in water are within the toxicity range or not. In aqueous media, DASPC22 forms nonfluorescent H-aggregates, but fluorescence is enhanced upon forming host-guest inclusion complexes with β-CD. At low ClO4− ions concentrations, fluorescence intensity further increases due to enhanced complex stability through hydrogen bonding. ONIOM-based quantum chemical calculations have supported this phenomenon. The enhancement of fluorescence intensity of DASPC22 in the presence of β-CD and a low concentration of ClO4− ions leads to the construction of a YES logic gate that would enable one to quantify ClO4− ions’ toxicity range in water. Dual-input-single-output AND and INHIBIT logic gates with low and high concentrations of ClO4− ions, respectively, have also been constructed. The present system could be useful in addressing safety concerns related to perchlorate contamination of water.