Iron and manganese in groundwater impair the quality of drinking water; however, the rates of iron and manganese removal with conventional aeration and rapid sand filtration (RSF) processes vary extensively. Five full-scale aeration–RSF processes in Nepal also showed varying efficiencies of iron and manganese removal; while the iron concentration was below the national standard (0.30 mg/L) in 31 out of the 37 treated waters, the manganese concentration was higher than the standard (0.20 mg/L) in all of the treated waters. Re-aeration and stirring of the treated water did not oxidize soluble manganese, and this caused the poor removal rates for manganese. Bench-scale dual-media filters comprising anthracite on top of sand/ceramic layers with dosages of poly aluminum chloride and chlorine worked well by removing coagulated iron in the anthracite layer and then removing manganese in the sand/ceramic layers. A manganese-oxide-coated ceramic filter provided the highest manganese removal from 1.10 mg/L to <0.01 mg/L, followed by manganese-oxide-coated sand and quartz sand. Increasing the pH from 7.5 to 9.0 stabilized the manganese removal. Therefore, we propose a re-design of the present treatment processes and the selection of suitable filter media for better removal of iron and manganese.