The Ministry of Environment of Korea promulgated Water Treatment Rule that had been effective from July 1, 2004 for the treatment plants larger than 100,000 m3/day. Effective dates are different depending on the size of water treatment capacity. The purposes of the rule are to improve control of viruses and microbial pathogens, specifically the protozoan Giardia, in drinking water. However, many water treatment plants that have been built under the regulation of filter effluent turbidity of 1.0 NTU before 1999 are not ready for the new rule which requires removal and/or inactivation of 3-log (99.9 percent) for Giardia and 4-log (99.99 percent) for viruses and the combined filter effluent turbidity of 0.3 NTU at the 95th percentile monthly, based on 4-hour monitoring for treatment plants using conventional treatment. Water treatment facilities are required to install new clear wells and to optimize each process from coagulation to filtration to provide multiple barriers of treatment to control pathogen occurrence in finished drinking water. This paper discusses general problems those water treatment plants have had and suggests possible solutions for the problems most water treatment facilities are facing now.