Under-cover soilless cultivation is an important technique of crop production. Due to the lack of contact with soil and precipitation, the root system of crops grown must be provided with water and all necessary nutrients in the form of a solution (nutrient medium). This nutrient medium needs to be fed in excess to ensure proper plant development and the expected qualitative and quantitative parameters of the crop yield, which means that in the case of, e.g., tomato cultivation, 20–80% of the supplied medium must be removed from the root system and managed. Uncontrolled discharge of this drainage water poses a significant threat to the environment, causing contamination of surface waters and groundwaters. The article presents the latest solutions for drainage water management as well as technologies and systems that allow saving water and fertilizers, and thus recovering elements. It also characterizes methods deployed for the treatment of overflow that enable its recirculation, its re-use for fertilization of other less demanding crops (including soil crops), and its final management in the form of a discharge to the natural environment. Due to depleting resources of adequate-quality water, increase in the prices of mineral fertilizers, and depletion of natural phosphorus deposits, the future trends in water and nutrients management in this cropping system aim at closing circuits of drainage water and recovering elements before their discharge into the natural environment. These measures are expected not only to protect the natural environment but also to reduce the costs of crop production.