To prevent the development of plant diseases, irrigation water needs to be disinfected. The commonly applied cleaning methods do not allow the possibility of activation and enrichment of irrigation water with nutrients. The target of this study is to develop an environmentally friendly method for disinfecting and activating irrigation water by treatment with high‐voltage discharges in an electro‐hydraulic installation. The study used the following materials and equipment: a high‐voltage installation with an electro‐hydraulic spark gap, an EnSURE luminometer (Hygiena) to measure the level of hygiene of water and its solutions, AquaSnap Total (AQ100X) test tubes (Hygiena) to determine the total amount of adenosine triphosphate (ATP) in water, and an ITAN ionomer (Tomanalit) for measuring nitrogen compounds in water. Experimentally the following optimal parameters and technological conditions were determined and substantiated to reduce irrigation water pollution from 1210 RLU to 73 RLU and increase water content of nitrogen compounds from 1.2 mg L‐1 to 8.4 mg L‐1: an operating voltage of 19.9 kV, a capacity 0.145 μF, and a number of discharges of 2860 pcs. Water disinfected with high‐voltage discharges will be useful for agricultural irrigation since it can serve as a nitrogen fertilizer, which does not have any harmful effect on the environment.