NO3− pollution in water and wastewater is a pressing global environmental issue, leading to the deterioration of water quality and an increased risk to human health. Herein, we present a three-dimensional (3D) flow-through electrode composed of electrodeposited Cu-Pd bimetallic catalysts on a nickel foam. The Cu-Pd bimetallic particles exhibited cluster-like shapes on the surface of the nickel foam. This electrode design enhanced the electrochemical activity of the NF/Cu63Pd37 electrode for NO3− reduction, as evidenced by linear sweep voltammetry (LSV) measurements. By tailoring the Cu-Pd ratio (Cu:Pd 0.63:0.37), the NF/Cu63Pd37 electrode showed the highest reactivity of NO3− reduction and selectivity (43.1 %) toward N2. Importantly, the NF/Cu63Pd37 electrode not only achieved over 99 % NO3− removal but also exhibited a higher kinetic rate constant of 1.44 h−1 in the flow-through mode. In contrast, in the flow-by mode, NO3− removal was 67.5 % with a lower reaction rate constant of 0.30 h−1. Furthermore, the NF/Cu63Pd37 electrode exhibited a reduced energy consumption (EEO) of 6.86 kWh m−3 order−1 in the flow-through mode, contrasting with 13.66 kWh m−3 order−1 in the flow-by mode. Moreover, the results also demonstrated successful NO3− remediation across various initial pH values (pH 3, 6, 9, and 11) and NO3− concentrations (100, 200, and 300 mg L−1). The results of this study highlight that the 3D Cu-Pd bimetallic flow-through electrode, with its high reactivity in reducing NO3−, marks a significant advancement in efficiently treating nitrate-contaminated water.