The impact of rainfall events on the sanitary indicator bacteria density of the shellfish-growing waters in Geoje Bay and Jaran Bay in Korea was investigated. The shellfish-growing area in Geoje Bay, which is a nearly closed basin, was not affected significantly, except near the stream mouth after 11.5 mm of rainfall in 1 day. However, most of the shellfish-growing water in the bay was polluted by fecal coliform bacteria after rain as heavy as 43.0 mm, and the levels of fecal indicator bacteria in some of the sea near the coast did not recover completely until 24 hours after the rainfall. By contrast, in Jaran Bay, which has no significant pollution source in the drainage area, although 9.3-490 MPN/100 mL of fecal coliform bacteria were detected near the stream mouth after rainfall of 33.5 and 81.0 mm, a very low level of the indicator bacteria was detected in the designated shellfish-growing area. During the investigation, the correlations between the sanitary indicator bacteria density and physical parameters, such as salinity and turbidity, were evaluated. Both the total coliform and fecal coliform densities were inversely correlated with salinity. Turbidity was positively correlated with the indicator bacteria density. The survey results suggest that for more efficient management of the shellfish-growing areas located in coastal areas, such as shellfish harvesting after rainfall, a detailed investigation of the effects of rainfall on the bacterial water quality in each growing area is needed.