The effects of two substrates, sugarcane bagasse (T-1) and paddy straw (T-2) on water quality and growth of Labeo fimbriatus were studied in mud-bottomed, manured cement tanks, in triplicate; a set of three tanks without substrate served as control (T-3). Addition of manure and substrate brought about a decrease in dissolved oxygen level, but it stabilized after 15 days, when the tanks were stocked with 30 fish each, fed at 3% body weight daily and reared for 90 days. Total ammonia content in substrate based treatments was relatively lower than in the control. Significantly higher nitrite-nitrogen was recorded in the control tanks. The total plate counts (TPC) of bacteria in water did not differ significantly between treatments and control. The overall mean value of TPC with substrate was higher in T-2 than in T-1. The mean phytoplankton density in water was the highest in T-1, followed by T-3 and T-2, whereas zooplankton density was the highest in T-1 followed by T-2 and T-3. The growth of fish was significantly (P < 0.05) higher in substrate-based tanks, the percentage increases over control being 30.44 (T-1) and 28.71 (T-2) respectively. Higher RNA, DNA and RNA:DNA ratios were recorded under T-1, followed by T-2 and T-3. Higher enzyme activity was observed in fish from substrate treatments, which was attributable to the additional nutrients derived through the biofilm. The results demonstrated that production of L. fimbriatus can be significantly increased by the introduction of biodegradable substrates into culture systems where fertilization and feeding are employed.