This study examined the effects on nitrate removal when adding sulfur granules and crushed seashells to a woodchip bioreactor treating aquaculture effluents. Using a central composite design, the two components were added at three levels (0.000, 0.125 and 0.250 m3/m3 bioreactor volume) to 13 laboratory-scale woodchip bioreactors, and a response surface method was applied to find and model the optimal mixture ratios with respect to reactor performance. Adding 0.125 m3/m3 sulfur granules improved the total N removal rate from 3.27 ± 0.38 to 8.12 ± 0.49 g N/m3/d compared to pure woodchips. Furthermore, the inclusion of crushed seashells together with sulfur granules helped to maintain the pH above 7.4 and prevent a production (i.e., release) of nitrite. According to the modeled response surfaces, a sulfur granule:crushed seashell:woodchip mixture ratio containing about 0.2 m3 sulfur granules and 0.1 m3 crushed seashells per m3 reactor volume would give the best results with respect to high N removal and minimal nitrite release. In conclusion, the study showed that N removal in woodchip bioreactors may be improved by adding sulfur granules and seashells, contributing to the optimization of woodchip performance in treating aquaculture effluents.