Nutritional stress caused by copper (Cu) deficiency or toxicity affects fruit production of citrus orchards worldwide, but this could be minimised by fine-tuned fertilisation in the orchards. Two experiments were performed aiming to evaluate the photosynthetic capacity and the antioxidant enzyme activities of Swingle citrumelo seedlings, grown in nutrient solution (NS) with two levels of nitrogen (N) in the first experiment (adequate-N and high-N) and two levels of calcium (Ca) in the second (low-Ca and adequate-Ca). Plants were then exposed to various Cu levels (low, medium and high) for 15 days. Plants under Cu-toxicity exhibited specific effects on reactive oxygen species formation and root-to-shoot plant signalling. Copper absorption was greater with increased Cu concentration in the NS, which reduced plant biomass accumulation, gas exchange measurements, the activity of nitrate reductase and affected Cu partitioning between roots and shoots. Despite these effects, oxidative stress induced by excess-Cu was reduced at the highest N dose when compared to control and, on the contrary, increased with low-Ca supply. Therefore, a rational supply of N or Ca minimises Cu-induced stress damages to roots and leaves of plants, by directly enhancing the antioxidant system and protecting the associated antioxidative enzyme activities, whilst maintaining photosynthesis.