Hydroponic systems are efficient systems for vegetable production where plants grow 30-50% faster than in soil. Because of the abundant nutrients, heat, and light, microalgae often thrive in hydroponic systems, especially those with a recirculating nutrient solution. Microalgae affect water quality parameters such as pH, dissolved oxygen, consumption of nutrients in the water, and can compete with the target vegetable. Microalgae can even act as buffers and prevent effective chemical disinfection. Therefore, they are generally accepted as a "weed" in hydroponic systems and great efforts are made to minimise algal populations in hydroponic systems.

However, microalgae can also be beneficial for plant growth. The oxygen produced by photosynthesis of microalgae prevents anaerobiosis in the root system of plants, thus preventing injury to plant roots. Microalgae also secrete various substances (such as phytohormones and protein hydrolysates) that can act as plant growth promoters and biofertilizers, especially during the early stages of plant growth, germination, and root development. The presence of microalgae can significantly improve the removal rate of dissolved solids, total nitrogen and total phosphorus from hydroponic wastewater. Some studies have also shown that the use of mineral fertilisers in hydroponic production could be reduced by the use of live microalgae in the nutrient solution and the quality characteristics of the vegetables, such as total soluble solids (Brix) and vitamin C, could be increased. Hydroponic vegetable production could be upgraded to an environmentally friendly and economically sustainable production system with the co-cultivation of microalgae.

In the Water2REturn project, microalgae and residual water after harvesting microalgae were tested in hydroponic growth of lettuce and tomato at the University of Ljubljana. The microalgae thrived in the hydroponic systems and the vegetables grew well in all treatments, with or without microalgae. At the end of the experiment, there was no statistical difference between the fresh weight of the lettuce heads, while the addition of treated - autoclaved - microalgae and the use of residual water after harvesting had a significant positive effect on the growth of the lettuce roots. In the experiment with tomatoes, the control treatment consumed 50% more mineral fertiliser compared to the addition of microalgae residual water (supernatant), while tomato yield was comparable, proving that algae improved the nutrient utilisation of the hydroponic system. Root system growth was significantly improved by the addition of microalgae or supernatant (residual) water to the hydroponic system.