Storm runoff is a growing concern against a background of increasing urban densification, land-use adaptation and climate change. In this study, a storm water management model was used to analyze the hydrological and water-quality effects of rain gardens (also known as bioretention cells) as nonpoint source control solutions in low-impact development (LID) practices for an urban catchment in the Nakagyo Ward area of Kyoto in Japan. The results of simulations with input involving Chicago hyetographs derived for different rainfall return periods (referred to as 3 a, 5 a, 10 a, 30 a, 50 a and 100 a) indicated the effectiveness of this arrangement, in particular for rainstorm 3 a, which exhibited the maximum contaminant reduction ratio (Total Suspended Solids (TSS) 15.50%, Chemical Oxygen Demand (COD) 16.17%, Total Nitrogen (TN) 17.34%, Total Phosphorus (TP) 19.07%) and a total runoff reduction volume of 46.56 × 106 L. With 5 a, the maximum number of flooding nodes was reduced to 87, demonstrating that rain gardens handle rainfall effectively over a five-year return period. There was a one-minute delay for 100 a, which again indicates that rain gardens support control of urban runoff and mitigate flooding. Such gardens were associated with reduced stormwater hazards and enhanced resistance to short-term rainstorms at the research site, and should be considered for urban planning in Kyoto and other cities all over the world.