Culinary tourism centers generate wastewater that requires proper treatment to meet quality standards before discharge into receiving water bodies. One suitable treatment technology is the intermittent slow sand filter (ISSF), which can be enhanced with a grease trap pre-treatment unit and a roughing filter. This study investigates the effectiveness of modified ISSF media—comprising sand mixed with either Anadara granosa shell fragments or activated carbon—in reducing BOD, COD, and phosphate concentrations in culinary center wastewater. Additionally, the study aims to determine the optimal ISSF design using Response Surface Methodology (RSM). The ISSF reactor was operated intermittently with a 48-hour detention time over 22 days. Wastewater quality parameters were analyzed using the SNI method, and experimental data were processed using an RSM optimal (custom) design. Independent variables included operational duration, bacterial augmentation with Bacillus sp. in the grease trap, and filter media type. The response variables were removal efficiencies of BOD, COD, and phosphate. Optimal treatment conditions were achieved using a sand and activated carbon media mixture, 1% Bacillus sp. addition, and an 11-day detention time, resulting in BOD, COD, and phosphate removal efficiencies of 62.50%, 72.54%, and 72.32%. Analysis of Variance (ANOVA, p < 0.05) of the 2FI model confirmed that all independent factors significantly influenced pollutant removal efficiency. These findings indicate that the proposed ISSF design offers a reliable and efficient approach for improving wastewater quality through integrated biological and physical treatment processes.