Removal of natural organic matter (NOM) and taste and odor problems in drinking water are a sensitive issue in municipal water treatment plants. This study investigated the effectiveness of ozone (O3) + granular activated carbon (GAC), O3 + hydroperoxide (H2O2) + GAC, and GAC processes using a pilot scale plant to remove NOM and geosmin (50–1,000 ng/L), and 2-methylisoborneol (2-MIB: 50–300 ng/L). In the O3 + GAC process, NOM-related parameters showed an average of 52% dissolved organic carbon (DOC) removal from 2 mg/L DOC influent, 99.3% haloacetic acids (HAAs) removal from 0.097 mg/L HAAs influent, and 100% removal from 0.05 mg/L bromide influent. Taste and odor removal rates were 94–100% for geosmin and 87–100% for 2-MIB. The O3 + H2O2 + GAC process removed an average of 55% DOC, 99.7% HAAs, 100% bromate, 94–100% geosmin, and 93–100% 2-MIB. The GAC process removed 46% DOC, 98.3% HAAs, 100% bromate, 83–100% geosmin, and 81–100% 2-MIB. Based on a comparison of the efficiencies and an economic analysis, the O3 + H2O2 + GAC process was determined to be the optimal system for removing NOM and taste and odor compounds.