The present study aimed to develop and characterize new heavy metal sensors functionalized by extracellular polymeric substances (EPSs) isolated from a Tunisian thermophilic microalga strain Graesiella sp. The elaborated sensor showed a highly homogeneous character and revealed a microstructural lamellar arrangement, high crystalline nature, and several functional groups. Electrochemical impedance spectroscopy (EIS) and acoustic wave sensing were used as sensing techniques to explore the ability of microalgae-EPS-functionalized sensors to detect cadmium and mercury as heavy metals. For impedimetric measurements, a two-dipole circuit was adopted and showed good-fitted results with a low total error. The acoustic sensor platforms showed good compatibility with EPS in adjacent water. For both EPS-functionalized sensors, metal ions (Cd2+, Hg2+) were successfully detected in the concentration range from 10−10 M to 10−4 M. Impedimetric sensor was more sensitive to Cd2+ at low concentrations before saturation at 10−7 M, while the acoustic sensor exhibited more sensitivity to Hg2+ over the full range. The results highlight a new potential alternative to use microalgae EPSs as a sensitive coating material for the detection of heavy metals. However, its use in a real liquid medium requires further investigation of its selectivity in the presence of other compounds.