In this study, hierarchically CuBTC, Fe-CuBTC and Zr-CuBTC MOFs for investigation of non-electroactive glyphosate compound (Gly) has been tested towards the best material for its detection by electrochemical sensors. The novel metallic/bimetallic Fe-Cu/Zr-Cu metal-organic framework (MOF) combined with 1,3,5-benzenetricarboxylic acid (BTC) are synthesized using hydrothermal reaction and used as modifiers. These MOFs were separately dropcasted on a glassy carbon electrode and non-electroactive Gly signals in the water environment were tested by cyclic voltammetry (CV), impedance measurement (EIS), and differential pulse voltammetry (DPV). Gly presences in water were recognized by the differences of currents in spiked and non-spiked Gly samples. Data showed the bimetallic Zr-CuBTC MOF is the most promising material for the detection of Gly using an electrochemical sensor. Morphological and structural studies showed the coordination of Cu2+ with the presence of Zr4+ ions with BTC ligands being highly porous framework with active surface area up to 1337 m2 g− 1, the pore diameter and pore volume increased to 1.75 nm and 0.687 cm3 g− 1, respectively. Under optimal conditions, the Zr-CuBTC/GCE sensor is able to indirectly detect Gly in a water environment at a detection limit as low as 9.10− 12 M. The developed sensor was employed to determine Gly in the real surface water samples collected from the Red River, North Vietnam. The results showed good recoveries (94.6–107.1%) which were in agreement with data obtained by liquid chromatography coupled tandem mass spectrometry (LC-MS/MS) measurements. These results demonstrate the possibility of using such MOF material in sensor applications for accessing the residues of trace pesticides contaminated in the natural water environment.