The rapid development of the textile industry has led to the discharge of large amounts of dyes into aquatic environments, such as rivers and lakes. Long-term exposure to these substances causes many adverse health effects. Therefore, compact, highly sensitive sensors that enable rapid, on-site assessment of water quality have received significant attention. High-performance SERS substrates were successfully fabricated by optimizing and controlling the thickness of the shell of core–shell Au@Ag NPs by using both experimental and FDTD calculations. Results on the individual and simultaneous detection of dyes demonstrate the potential of Au@Ag NPs as substrates for environmental applications, where dyes exist in complex forms. Detection limits for the three organic substances, rhodamine B, crystal violet, and methyl orange, were 1.89 × 10^–12, 6.57 × 10^–13, and 1.08 × 10^–9 M, respectively, demonstrating a significant improvement in sensitivity compared to single Au and Ag NPs. At the same time, tests in Han River water also demonstrated the high applicability of the SERS Au@Ag NP substrate in real samples. This is one of the advances in the development of SERS-based sensors for environmental applications. For the first time, the core–shell Au@Ag NPs were evaluated for their capabilities, including simultaneous detection and sensing in real water samples. This is of great significance in the application of this technique beyond the laboratory scale.

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