Recirculation aquaculture systems (RASs) operated at low water exchange rates are known to accumulate minerals in the water. This study examined the dietary mineral requirement and metabolism in common carp reared in RAS of contrasting water exchange rates. Two independent RAS (water exchange rates, 70 vs. 2000 L/kg feed) and five experimental diets with graded levels of micro-mineral premix inclusion (0.0, 0.3, 0.6, 1.0 and 1.5%) were tested in a 2 × 5 factorial arrangement. Common carp fingerlings (8.5 g) were reared in either of the RAS and fed the experimental diets in triplicates for 8 weeks at 24 °C. Water quality, fish growth, body composition, tissue mineral concentrations, blood haemoglobin and haematocrit levels, biochemical and molecular markers of oxidative stress, mineral uptake and metabolism were studied. RAS operated at low water exchange rate showed significantly high conductivity, nitrate, nitrite and dissolved mineral concentrations in water. A tendency for higher growth, significantly higher whole body mineral levels except Cu and Zn were observed in fish reared in RAS with high accumulation of minerals (H-RAS). Of the micro-minerals studied, effect of RAS on the minimal dietary inclusion level was significant only for Se; lower in fish reared in the H-RAS (0.28 mg/kg) compared to L-RAS (0.32 mg/kg). Increasing premix inclusion decreased growth and feed efficiency, increased the whole body concentration of Cu, Se and Zn, while Fe and Mn were unaffected. Plasma P, Ca, K and Mn were higher and haematocrit was lower in H-RAS reared fish; plasma mineral levels were also influenced by premix inclusion. Enzymes involved in micro-mineral uptake and metabolism (ferric reductase, cupric reductase and alkaline phosphatase) and oxidative stress markers (glutathione peroxidase, catalase, glutathione reductase and glutathione S-transferase) were analysed in gill, intestine and liver. In fish reared in H-RAS, reduced glutathione peroxidase (GPx) and increased glutathione reductase (GR) activities were observed in liver and intestine, respectively. Activity of GPx in all the analysed tissues increased with premix supplementation. Differential regulation in mRNA expression of molecular markers related to micro-mineral uptake, metabolism and oxidative stress were observed in the tissues in response to RAS and premix inclusion. To conclude, fish reared in high accumulation RAS had higher mineral levels in whole body and vertebrae, but did not result in a lower estimate of micro-minerals, except for Se. Difference in rearing system had multiple effects on the physiology and metabolism of fish on the whole, apart from mineral balance alone.