This study compared the effect of three sources of carbohydrates: sugar, wheat and malt flours, on water quality, water consumption, bacterial load, growth and flesh quality of Nile tilapia. Adults (120.6 ± 0.64 g) were stocked in 1.2‐m3 fibreglass tanks at a rate of 25 fish/m3. Carbohydrates were added to the biofloc tanks at a C:N ratio of 20:1. Water flow in the non‐biofloc control tanks was adjusted to 0.6 L/day. The 105‐day experiment was conducted in triplicates. Results showed that biofloc treatments (BFT) with zero water exchange had significantly higher mean total ammonia, nitrites, nitrates, alkalinity, total suspended solids and lower pH than the control treatment. The sugar BFT had the highest floc volume. Growth parameters and feed conversion ratio did not differ significantly among treatments. However, tilapia in the malt flour and control treatments had close values. Gross fish yield was higher (p < .05) in the control than the BFT treatments. Water consumption/kg tilapia produced in the control was 42 times higher than the BFT groups. Protozoa dominated the biofloc biota, and wheat flour was the best in harbouring higher bacterial populations in the gut. Protein content and ∑n‐3 fatty acids were highest in the wheat flour biofloc, while malt flour biofloc had the highest lipids. The sugar biofloc had the highest n‐3/n‐6 ratio. Tilapia muscles in the malt flour and control treatments had the highest protein and lipid contents respectively. Tilapia muscles in the wheat flour BFT had the highest ∑n‐3 fatty acids and n‐3/n‐6 ratio. It can be concluded that farming tilapia in BFT using malt or wheat flours as carbon sources is more economical in saving great amount of water with minimal discharge of pollutants without affecting tilapia growth or flesh quality.