The scarcity and contamination of water, aggravated by the effects of Climate Change, endanger the food supply, cause health problems to humans, and are a critical concern. New research has been carried out to improve the quality of water used in the agricultural sector. One of them is the technology of non-thermal plasma (NTP) generated by corona discharges using air as a working gas. In this study, the NTP is applied directly and causing the activation to three water sources: potable, wastewater from poultry farming, and rain, on the legume “lentil.” The results show that the NTP applied to the different water conditions modifies the legume structure, obtaining a better germination and growth rate. In particular, it found that the best condition to stimulate the plant structure growth is using wastewater from poultry activities, which NTP activates. Likewise, it identified the internalization of pathogenic microorganisms such as Escherichia coli and Salmonella typhimurium since the early development of the plant. The bacteria reduction after NTP application is detected due to the effect of the reactive species generated by the NTP. The NTP application for water activation can represent an alternative to solve the demand for food since the development of the structures of legumes, particularly of lentils, is promoted.