Rainwater collected from a rooftop rainwater harvesting (RWH) system is typically not considered suitable for potable uses, primarily because of poor microbial quality. The quality of stored rainwater, however, can be improved through basic design and maintenance practices during the construction and operation of an RWH system. This paper presents the microbial analysis of rainwater in two RWH systems installed at the Seoul National University Campus in South Korea. Rainwater samples were collected at different locations within each system and analyzed for total and fecal coliforms, Escherichia coli, and heterotrophic plate count bacteria. Within their storage tanks, water quality improved horizontally from inlet to outlet points, and higher quality was observed at the supply point (located about 0.5 m from the base of the tank) than at the surface or bottom of the tank. First-flush rainwater was found to be highly contaminated but rainwater quality improved following about 1 mm of precipitation. The catchment surface also had a significant effect on the quality of rainwater; samples collected from a rooftop exhibited better microbial quality than from a terrace catchment. Better water quality in underground tanks (dark storage conditions) compared to open weirs/filters (exposed to natural light) demonstrated the importance of storage conditions. Water quality also improved with longer storage, and a decrease of 70% to 90% in microbial concentrations was observed after about 1 week of storage time. The findings of this study demonstrate that the microbial quality of harvested rainwater can be improved significantly by the adoption of proper design and maintenance guidelines such as those discussed in this paper.