Partial substitution of nitrate (NO3-) with chloride (Cl-) in the nutrient solution supplied to tomato crops (beefsteak and cherry types), grown in a closed hydroponic system, maintained nitrogen (N)- and carbon (C)- assimilation status in plants despite N-supply limitations. Lowering NO3- ions (90% of total N) supply to 2/3 of the standard recommendations, which was electrochemically compensated for by an equivalent increase of the Cl- concentration in the replenishment nutrient solution (RNS), increased N use efficiency (kg produce kg−1 N supply) and decreased NO3- in the drainage without compromising growth, yield and nutritional quality. Tomato plants supplied with Cl--amended RNS increased leaf Cl- content to macronutrient level (35 mg g−1 dry weight), retaining photosynthetic rates and crop yield potential at lower stomatal conductivity and transpiration. Nutrient to water uptake ratios (mass of nutrient per water volume absorbed), which are commonly termed ‘uptake concentrations’, were defined in different cropping seasons and ranged as follows: 12.1–13.5 (Nitrogen- NO3-+NH4+), 1.25–1.35 (Phosphorus-P), 6.1–6.3 (Potassium-K), 3.6–4.0 (Calcium-Ca), 1.0–1.3 (Magnesium-Mg, mmol L−1), 13.0–14.3 (Iron-Fe), 7.6–8.4 (Manganese-Mn), 5.1–5.2 (Zinc-Zn) and 0.7–0.9 (Copper-Cu, μmol L−1). The levels of N and Cl- supply had no impact on the uptake concentrations. This study suggests that replacing 1/3 of the standard NO3- supply by Cl- in closed hydroponic tomato crops enhances N use by two-fold and eliminates NO3- losses to one-half, with no significant effects on assimilation processes and fruit biomass production, suggesting that Cl- at appropriate concentrations is not only an essential micronutrient but also a beneficial macronutrient. The obtained uptake concentrations may be used through on-line operating decision support systems to optimize nutrient supply in hydroponic cultivations in Mediterranean greenhouses.