In situ detection of Cu2+ ions in the effluent from thin-film transistor-liquid crystal display (TFT-LCD) manufacturing facility has been successfully achieved using thiol-capped CdS/ZnS quantum dots (QDs) as the fluorescence probes. Three types of ligands, including L-cysteine (LC), mercaptosuccinic acid (MSA), and thioglycolic acid (TGA), were used as capping agents for stabilizing and functionalizing the QDs. Fluorescence quenching of the QDs by Cu2+ ions was well fitted by the Stern–Volmer equation, indicating a static quenching process. Interaction between the Cu2+ ions and the thiol-based capping agents to form Cu–S bonding was responsible for the nonradiative decay. The thiol-capped probes exhibited low detection limits (0.016–0.063 mg L−1), high recovery (81.7–114.5%), good precision (relative standard deviation = 0.36–4.56%), and suitable accuracy for the detection of Cu2+ ions in the field samples, even though those that contained Ca2+, Mg2 +, Na+, K+, and NH+ 4 ions, which were 300–16,600 times higher in concentration than the target. These results clearly verify the feasibility of using the QDs as an early warning system for assisting TFT-LCD manufacturing facilities in compliance with strict effluent standards (0.15 mg L−1). Among the three types of thiol-capped QDs, the TGA-capped probes were the most sensitive and the LC-capped probes exhibited the highest errors. Substantial loading of the small TGA ligands on the surface and competitive complexation of the amino groups with Cu2+ ions are responsible for the benefits and the consequences of the TGA- and LC-capped QDs for Cu2+ sensing, respectively.