In this work, an electrochemical system combined with low-cost UV-LEDs was implemented for the inactivation of Escherichia coli and Pseudomonas aeruginosa. The individual elimination of these bacteria was followed by plate counting and flow cytometry, as complementary techniques to establish the cell inactivation and non-viability, respectively. The contribution of the different parts of the disinfection system (anode, cathode, and light) was determined. In addition, the efficiency of the UV-LEDs/GDE/DSA system in the disinfection of an irrigation water sample was studied. It was found that the combination of the electrochemical system with UV-LEDs was highly synergistic (φ > 7), having low electric energy consumptions per order of magnitude (EEO: 1.13 × 10–2 and 1.55 × 10–2 kWh/m3 order). Moreover, some differences in the inactivation kinetics and synergy between E. coli and P. aeruginosa were observed and linked to the structural/morphological characteristics of the two bacteria. Remarkably, the electrochemical system combined with low-cost UV-LEDs inactivated both target microorganisms after only 2 min of treatment. The flow cytometry analyses evidenced the damage to the cell membrane of the bacteria by the simultaneous and synergistic action of the electrogenerated H2O2 and active chlorine species (ACS), plus the attacks of photo-generated reactive oxygen species. This synergistic combination in the UV-LEDs/GDE/DSA system demonstrated remarkable efficiency in the disinfection of an irrigation water sample, achieving the elimination of culturable bacteria in 45 min of treatment. The results of this research demonstrated the capacity and great potential of an easy combination of electrochemistry with UV-LEDs as an alternative system for the elimination of gram-negative bacteria in water.