Microwave spectroscopy has been identified as a novel and inexpensive method for the monitoring of water pollutants. Integrating microwave sensors with developed coatings is a novel strategy to make the sensing system more specific for a target contaminant. This study describes the determination of copper and zinc concentration in water in both laboratory-prepared and acquired mine water samples from two abandoned mining areas in Wales, UK. Uncoated sensors immersed in samples spiked with 1.25 mg/L concentrations of copper and zinc, using the standard addition method, were able to quantify the concentration at 0.44 GHz with a strong linear correlation (R2 = 0.99) for the reflection coefficient magnitude (|S11|). Functionalised microwave sensors with l-cysteine, chitosan and bismuth zinc cobalt oxide-based coatings have shown improvement in the sensing performance. Specifically, the linear correlation at 0.91–1.00 GHz between |S11| and a polluted water sample spiked with Cu showed a higher (R2 = 0.98), sensitivity (1.65 ΔdB/mg/L) and quality factor (135) compared with uncoated sensors (R2 = 0.88, sensitivity of 0.82 ΔdB/mg/L and Q-factor 30.7). A Lorentzian peak fitting function was applied for performing advanced multiple peak analysis and identifying the changes in the resonant frequency peaks which are related to the change in metal ion content. This novel sensor platform offers the possibility of in situ monitoring of toxic metal concentrations in mining-impacted water, and multiple peak features, such as area, full width half maximum, centre and height of the peaks, have the possibility to offer higher specificity for similar toxic metals, as between copper and zinc ions.