Full factorial central composite design (CCD) and response surface methodology (RSM) were used to optimize and investigate the effects of major operational parameters such as organic strength, total suspended solids (TSS), and hydraulic loading rate (HLR) of the influent wastewater, which influenced the efficiency of organics (Chemical oxygen demand (COD)) removal from dairy wastewater using horizontal subsurface flow macrophyte-assisted vermifilter (HSSF-MAVF). The model obtained from RSM analysis was a quadratic polynomial model with a R2 value of 0.99. The optimum condition for the maximum COD removal was obtained at organic strength of 2550 mg/L, TSS concentration of 950 mg/L, and HLR of 1 m3/m2/d. Furthermore, at optimum conditions, COD removal effectiveness of 92.3% was achieved against the predicted COD removal rate of 95.3%. Similarly, validation of the model with real dairy wastewater has given minimal error (2.8%) against the predicted COD removal efficiency. The research also investigated the impact of hydraulic retention time (HRT) on the vermifiltration and interactive effects of operational parameters on clogging and its impacts on the efficiency of organics removal. The findings demonstrated that vermifiltration at a higher value of operational and design parameters created severe clogging and ponding of wastewater in the filter bed and had a detrimental effect on the rates of organics removal. With the increase in HRT, the treatment performance of the vermifilter improved. Removal efficiencies for COD, TN, and TP were 29%, 7%, and 10% higher, respectively, at an HRT of 9.8 h compared to 2.7 h.