The study was designed to assess the effects of periphyton grown on different substrates on water quality and production of major carps cultured in zero water exchange system. Three experimental treatments included; T1 (Control): without substrate, T2: using PVC pipes substrates, T3, using Bamboo poles substrates. Fish seed of Labeo rohita: Cirrhinus mrigala and Gibelion catla were stocked in cemented tanks in 1:1:1 ratio at stocking density of 3 fishm-2 for 60 days period. Survival rate of L. rohita, C. mrigala and G. catla was significantly higher (p<0.05) in substrates based treatments. In T1, T2 & T3, it was found to be 34.09%, 81.82% & 90.91% for L. rohita; 22.73%, 100.0% & 100.0% for C. mrigala and 36.36%, 90.91% & 100.0% for G. catla respectively. Total fish biomass of L. rohita, C. mrigala and G. catla harvested at the end of trial was 2.24, 4.32 and 1.42 times higher in treatment with bamboo poles as substrates and 1.18, 3.64 and 0.75 time higher in PVC pipes based treatment than that of control. Concentration of ammonia and nitrite was found to be significantly low in treatments with periphyton than control. High fish survival in periphyton based systems can be attributed to bioremediation through bioprocesses of their ubiquitous microbial biofilms.