Aquaponics is a recirculating technology that combines aquaculture with hydroponics. It allows nutrients from fish waste to feed plants and thus saves water and nutrients. However, there is a mismatch between the nutrients provided by the fish waste and plant needs. Because of this, some nutrients, notably N, tend to accumulate in the aquaponic water (APW or AP water). The aim of this study was to investigate how APW, which is depleted of P and K but still rich in N, could be further utilized. APW was used in a mesocosm and compared with APW from the same source that had been supplemented with macro-nutrients (complemented AP water or CAPW) and a hydroponic control (HC). Mizuna (M) and rocket salad (R) were used as short-cycle vegetable crops in a NFT system. The results revealed that the low production potential of APW was mainly caused by the lack of P and K. If these were supplemented, the yields were comparable to those in the HC. M yield in CAPW was significantly higher than that of HC, probably due to biostimulant effects connected to the organic components in the water as a result of fish farming. Water type, cultivation density, and intercropping significantly influenced the qualitative characteristics of the crop in terms of antioxidant compounds and minerals. Nitrate content in vegetables was lower than European regulation limits. The extended use of APW is viable if the missing nutrients are supplemented; this could be a strategy to increase the efficiency of water and nitrogen use, while further reducing environmental impact