A gold nanorod (AuNR) based colorimetric probe was reported for the rapid and selective detection of Cu²⁺ ions. The probe was fabricated by functionalizing cysteine (Cys) onto AuNR (Cys-AuNR) with an aspect ratio of 2.3. The strong coordination of Cu²⁺ with cysteine resulted in a stable Cys–Cu–Cys complex, and induced the aggregation of the colloidal nanorods along with a rapid colour change from blue-green to dark gray. Potential factors affecting the performance of the probe for the detection of Cu²⁺ were carefully optimized, including the pH value of the buffer media, the concentration of cysteine, and the kinetics for the coordination of Cu²⁺ with Cys-AuNR. Under optimal conditions, the developed colorimetric method gave a linear range of 1–100 μM for Cu²⁺, and a detection limit (3s) of 0.34 μM. Moreover, the developed method exhibited excellent selectivity for Cu²⁺, and quantitative spike-recoveries from 90% to 107% in environmental water samples. The proposed colorimetric approach can in principle be used to detect other metal ions by functionalizing various specific ligands onto the AuNR that can selectively bind the other target metal ions.