A colorimetric assay has been developed for parallel detection of Cd(2+), Ni(2+) and Co(2+) utilizing peptide-modified gold nanoparticles (P-AuNPs) as a sensing element based on its unique surface plasmon resonance properties. The functional peptide ligand, CALNNDHHHHHH, was self-assembled on gold nanoparticles (AuNPs) to produce P-AuNPs probe. The P-AuNPs probe could be used to simultaneously detect and showed different responses to the three ions Cd(2+), Ni(2+) and Co(2+) in an aqueous solution based on the aggregation-induced color change of AuNPs. The method showed good selectivity for Cd(2+), Ni(2+) and Co(2+) over other metal ions, and detection limit as low as 0.05 μM Cd(2+), 0.3 μM Ni(2+) or 2 μM Co(2+). To simultaneously (or parallel) detect the three metal ions coexisting in a sample, EDTA and imidazole were applied to mask Co(2+) and Ni(2+) for detecting Cd(2+), glutathione and EDTA were applied to mask Cd(2+) and Co(2+) for detecting Ni(2+), and glutathione and imidazole were applied to mask Cd(2+) and Ni(2+) for detecting Co(2+). Finally, the simple and cost-effective probe could be successfully applied for simultaneously detecting Cd(2+), Ni(2+), and Co(2+) in river water. Because this novel P-AgNPs-based probe design offers many advantages, including simplicity of preparation and manipulation compared with other methods that employ specific strategies, the sensing system shows potential application in the developing region for monitoring water quality.