This study aimed to investigate the effects of typhoons and dust storms on harvested rainwater quality. Rainwater samples were collected from the rainwater harvesting systems in northern Taiwan between September 2010 and April 2013. There were five typhoons and one dust storm that hit Taiwan during this period. Harvested rainwater was analyzed, including pH, electrical conductivity, turbidity, alkalinity, total organic carbon (TOC), acute biotoxicity test, and concentration of 13 metals and three anions. Results of harvested rainwater of the dust storm showed it had higher pH, turbidity, TOC, Na, Mg, Ca, Cl−, NO3− and SO42− than normal rainwater. Conversely, due to strong winds and dilution effect, most of the ion concentrations in harvested rainwater during typhoons were lower than in normal rainwater. In addition, biotoxicity in harvested rainwater during the dust storm and typhoons was not significantly different from that of normal rainwater.