Low nutrient and high pH of circulating water represent two of the main issues to overcome for a successful combination of aquaculture and hydroponics in aquaponics offering a sustainable and circular economy solution for vegetable production. The purpose of this study was to screen the tolerance of four herbs to high pH and low nutrient concentration in hydroponics, i.e., green and red basils, mint, and rocket salad, with a focus on plant yield and nutraceutical aspects. Results highlighted green basil as the most tolerant species to low nutrient and high pH conditions followed by mint. On the contrary, negative effects from high pH and low nutrient were reported on red basil and especially rocket salad, which strongly affect their marketability parameters. Rocket salad fresh biomass was more than halved under the combination of high pH and low nutrients. Results on green and red basil showed the importance of testing the tolerance to these agronomic conditions at both species and variety levels. Despite the reduction in biomass, leaf pigments were not influenced by high pH and low nutrients and therefore can be considered parameters of minor importance for the evaluation of these species. In conclusion, the tolerance of green basil and mint to high pH and low nutrients under hydroponic conditions has been highlighted. Further investigation coupled with fish farming will be able to reinforce the convenience of using these species for aquaponics.