Algal problem in drinking water treatment is being gradually increased by causing deterioration of water supplies therefore, especially taste and odor compounds such as geosmin and 2-MIB occur mainly aesthetic problem by its unpleasant effects resulting in the subsequent onset of complaints from drinking water consumer. Recently, geosmin and 2-MIB are detected frequently at abnormally high concentration level. However, conventional water treatment without advanced water treatment processes such as adsorption and oxidation process, cannot remove these two compounds efficiently. Moreover, it is known that the advanced treatment processes i.e. adsorption and oxidation have also several limits to the removal of geosmin and 2-MIB. Therefore, the purpose of this study was not only to evaluate full scale nanofiltration membrane system with $300m^3/day$ of permeate capacity and 90% of recovery on the removal of geosmin and 2-MIB in spiked natural raw water sources at high feed concentration with a range of approximately 500 to 2,500 ng/L, but also to observe rejection property of the compounds within multi stage NF membrane system. Rejection rate of geosmin and 2-MIB by NF membrane process was 96% that is 4% of passage regardless of the feed water concentration which indicates NF membrane system with an operational values suggested in this research can be employed in drinking water treatment plant to control geosmin and 2-MIB of high concentration. But, according to results of regression analysis in this study it is recommended that feed water concentration of geosmin and 2-MIB would not exceed 220 and 300 ng/L respectively which is not to be perceived in drinking tap water. Also it suggests that the removal rate might be depended on an operating conditions such as feed water characteristics and membrane flux. When each stage of NF membrane system was evaluated relatively higher removal rate was observed at the conditions that is lower flux, higher DOC and TDS, i.e., $2^{nd}$ stage NF membrane systems, possibly due to an interaction mechanisms between compounds and cake layer on the membrane surfaces.