This study presents an ultra-sensitive dual-core photonic crystal fiber-based surface plasmon resonance (PCF-SPR) sensor for the detection of waterborne pathogens through refractive index (RI) variation. The proposed sensor integrates a bimetallic coating of silver and titanium dioxide (Ag–TiO₂). Silver ensures sharp plasmonic resonance, and TiO₂ enhances chemical stability and coupling efficiency. This dual-core configuration allows for increased interaction between the core-guided modes and the plasmonic interface. As a result, the sensor’s sensitivity improves significantly. The sensor can accurately detect analytes with an RI value of 1.28 to 1.43. It demonstrates a maximum wavelength sensitivity (WS) of 107,000 nm/RIU, an amplitude sensitivity (AS) of 2209.21 RIU⁻¹, a wavelength resolution of 9.35 × 10⁻⁷ RIU, and a figure of merit (FOM) of about 520. These results support the sensor’s ability to identify the presence of different pathogenic contaminants, such as E. coli, Vibrio cholerae, and Bacillus anthracis, based on their unique RI properties. This optimized design, high resolution, and potential for real-time detection enable this sensor to be a promising solution for environmental monitoring applications.