This study compares Raffia hookeri seeds extracts and LemnaTrisulca (Duckweed) as disinfectant in water treatment. Raffia hookeri and duckweed were obtained within Makurdi, Nigeria. While the raw water samples were taken from River Benue for the study. Laboratory analysis was carried out using dosage, pH, temperature, initial concentration, and flocculation speed as variables. Filtrate and powder from Raffia hookeri and LemnaTrisulca were used. The result revealed that extracts from the filtrates at 0.3 ml concentration gave the optimum, removing 98.2% and 82.9 % of bacteria for Raffia hookeri and duckweed respectively. For the powder, optimum conditions with respect to bacteria removal were; Dosage = 0.2 ml, pH = 3, Temperature = 30 °C, Initial concentration = 633 FTU and flocculation speed =90rev/min with average percentage removal of 91.1 % and 83.7 % for Raffia hookeri and Duckweed respectively. In conclusion, filtrate obtained from Raffia hookeri gave a greater removal of bacteria for disinfection of water.