Cultivating high-value deposit feeders such as sea cucumbers on solid waste from intensive aquaculture is an innovative approach to turn potential nutrient pollution into a resource. Carbon supplementation to increase the carbon to nitrogen ratio (C:N) of the nitrogen-rich aquaculture waste has been demonstrated to support higher deposit feeder biomass, but commercially viable carbon sources remain to be tested. This experiment investigated the performance of laboratory grade cellulose and bagasse, an agricultural waste product, to improve growth and nutrient utilization from milkfish aquaculture waste in juveniles of the sea cucumber Holothuria scabra. Supplementation with bagasse supported a significantly higher final biomass density (205.71 ± 11.08 g m−2, mean ± SE) than waste without carbon supplementation (p = 0.027). For the first time, a species-specific tropHic enrichment factor (Δ13Corg) was applied in stable isotope analysis of feed sources by H. scabra (Δ13Corg of 2.56 ± 0.96‰ (mean ± SD) for the internal organs and 4.31 ± 0.96‰ for the body wall). Results indicated that sea cucumbers were able to assimilate carbon directly from the cellulose. Bagasse supported higher uptake of carbon from aquaculture waste, thus identifying it as a viable resource to improve bioremediation by deposit feeding sea cucumbers in integrated aquaculture. While illustrating the importance of nutrient balances for bioremediation, questions remain about the roles of direct feeding by deposit feeders vs. the decomposition by microbial communities.