Periphyton community grown on submerged substrate in water could serve as a preferred natural food item to herbivorous and omnivorous fish and crustacean species. To determine the optimum substrate area for the growth of periphyton biomass serving as natural food and to reduce the requirement of pellet feed quantity, a 150-day pond experiment was conducted with four treatments of brackishwater polyculture: total feeding and no periphyton substrate (P0), and partial feeding with periphyton grown on nylon net substrate equivalent to 50 (P50), 75 (P75) and 100 (P100) % of pond surface area. Each treatment had three randomly assigned replicate ponds (50 m2). After 15 days of substrate fixation in the surface layer of ponds up to 50 cm water depth, stocking was made with seeds of Mugil cephalus Linnaeus, 1758, Planiliza parsia (Hamilton, 1822), Chanos chanos (Forsskål, 1775) and Penaeus monodon Fabricius, 1798 at 1800, 18000, 2000 and 30,000 number ha−1, respectively. A low-cost pellet feed (30.76% crude protein) was provided at 6–3% of fish biomass per day. Dry matter (DM) of periphyton biomass was estimated from each replicate pond under P50, P75 and P100 from 15 × 15 cm2 net substrate, and then total periphyton DM was calculated according to the substrate surface area at 15-day intervals. Then, the total periphyton biomass was divided to find out daily DM availability. The feed amount in P50, P75 and P100 ponds was reduced proportionately to the equivalent daily periphyton DM availability and the feeding at this reduced quantity was continued for 15 days. The experiment revealed significantly lower levels of nitrogenous and phosphorus compounds, and dissolved organic carbon content in water of P75 and P100, compared to that of P0 and P50 (P < 0.05) and there were interaction effects of experimental period and periphyton substrate area on these parameters. All the species had an increasing growth pattern with experimental period and there was an interaction effect of experimental period and periphyton substrate area on growth of these species, indicating periphyton had positive effects. The highest specific growth rate was recorded in P. monodon and the lowest was in M. cephalus. Pooled survival of fishes and shrimp, and total productivity did not differ among treatments (P > 0.05). Although, the highest level of feed reduction (42%) by the utilization of periphyton biomass was in P100, P75 performed better in terms of productivity and economic return with 30% feed reduction in polyculture. Similarly, there was 26–41% reduction in feed conversion ratio with the highest level being in P100 (41%), followed by P75 (40%) in comparison to P0. Moreover, carcass composition of cultured fishes and shrimp indicated that periphyton based systems with partial feeding could meet up the nutrient requirement of the animals with no negative effects in comparison to the feed-based system. Therefore, this study suggests that provision of periphyton substrate equivalent to 75% of pond surface area along with partial feeding is the most appropriate approach for achieving higher return with environmental sustainability in brackishwater polyculture.