In this work, a guided shear horizontal mode surface acoustic wave (SH-SAW) sensor, fabricated by patterning gold (Au) interdigitated electrodes (IDE) on a 64° YX-LiNbO3 based piezoelectric substrate, was used for the detection of heavy metal compounds. A flow cell, with a reservoir volume of 3μL, which employs inlet and outlet valves for the microfluidic chamber and polydimethylsiloxane (PDMS) based microfluidic channels, was also designed and fabricated using an acrylic material. The frequency based response of the SAW sensor toward varying concentrations of heavy metal compounds such as lead nitrate (PbNO3) and cadmium nitrate (CdNO3) were investigated. As the surface acoustic wave propagates on the substrate, between input and output IDEs, a shift in the resonant frequency of the SAW device was observed due to the change in velocity of the wave caused by the varying concentrations of the test analytes. The results obtained demonstrated the capability of the system to detect picomolar level concentrations. The response of the SAW sensor is analyzed and presented in this paper.