Nitrogen is an element present on Earth in different forms, such as gaseous in the air, dissolved in water, immobilized in the soil, as well as biologically bound in all living organisms. The transition from one form to another constitutes the nitrogen cycle. Current agricultural systems rely on nitrogen fertilizers, which represent the reactive or biologically available nitrogen in soil. The excessive presence of reactive nitrogen in the environment has become a threat to soil, water, and air. The increasing demands for food in the world are associated with significant increase in nitrogen fertilizers inputs which threatens the environment and living organisms. The quantities of nitrogen used per capita in developed countries exceed those in developing countries. However, developed countries are regulated by restrictions of fertilizers inputs in agriculture, whereas such regulations do not exist in most of the developing countries. The need to resort to alternative and eco-sustainable strategies to mitigate the pollution related to human activities, is increasingly evident. This review aims to highlight the fate of nitrogen through the main agricultural practices in modern agriculture. Special attention was given to rocket (Eruca sativa) which is considered a nitrate hyper-accumulator and was used as a case study in the present review. Finally, some eco-sustainable solutions, useful for mitigating or preventing the excessive release of harmful forms of nitrogen into the environment, were also discussed.