Domestic wastewater discharge is the major source of pollution in Malaysia. Phytoremediation under hydroponic conditions was initiated to treat domestic wastewater and, at the same time, to resolve the space limitation issue by installing a hydroponic system in vertical space at the site. Water hyacinth (WH) was selected in this study to identify its performance of water hyacinth in removing nutrients in raw sewage under batch operation. In the batch experiment, the ratio of CODinitial/plantinitial was identified, and SPSS ANOVA analysis shows that the number of plant size factors was not statistically different in this study. Therefore, four WH, each with an initial weight of 60 ± 20 g, were recommended for this study. Throughout the 10 days of the batch experiment, the average of COD, BOD, TSS, TP, NH4, and color removal was 73%, 73%, 86%, 79%, 77%, and 54%, respectively. The WH biomass weight increased by an average of 78%. The plants have also improved the DO level from 0.24 mg/L to 4.88 mg/L. However, the pH of effluent decreased from pH 7.05 to pH 4.88 below the sewage Standard B discharge limit of pH 9–pH 5.50. Four WH plant groups were recommended for future study, as the COD removal among the other plant groups is not a statistically significant difference (p < 0.05). Furthermore, the lower plant biomass is preferable for the high pollutant removal performance due to the fact that it can reduce the maintenance and operating costs.