The progressive increase in nitrate’s (NO3−) presence in surface and groundwater enhances environmental and human health risks. The aim of this work is the fabrication and characterization of sensitive, real-time, low-cost, and portable amperometric sensors for low NO3− concentration detection in water. Copper (Cu) micro-flowers were electrodeposited on top of carbon screen-printed electrodes (SPCEs) via cyclic voltammetry (with voltage ranging from −1.0 V to 0.0 V at a scan rate of 0.1 V s−1). The obtained sensors exhibited a high catalytic activity toward the electro-reduction in NO3−, with a sensitivity of 44.71 μA/mM. They had a limit of detection of 0.87 µM and a good dynamic linear concentration range from 0.05 to 3 mM. The results were compared to spectrophotometric analysis. In addition, the devices exhibited good stability and a maximum standard deviation (RSD) of 5% after ten measurements; reproducibility, with a maximum RSD of 4%; and repeatability after 10 measurements with the RSD at only 5.63%.