Information on the effects of inter-annual variations in climatic factors on fecal coliform levels in coastal waters is scarce. We used 11 years (1990-2001) of rainfall, water temperature, Pearl River stage and salinity data to assess the effects of the 1991-1992 and 1997-1998 El Nino events on fecal coliform levels in Mississippi Sound. El Nino-Southern Oscillation had major effects on Pearl River stage and water quality in the Sound. The geometric mean fecal coliform number differed among years (P = 0.0001), being highest during 1991-1992 El Nino years (14.22 MPN per 100 ml) and lowest during 1999-2000 La Nina years (<1.8 MPN per 100 ml). Mean salinity varied among years (P = 0.0001) from 9 ppt (1991-1992) to 21 ppt (1999-2000). Mean water temperature was lowest in 1997-1998 (14.5 degrees C) and highest in 1998-2000 (19.4 degrees C). Pearl River stage differed among years (P = 0.0001), ranging from 1.96 m (1999-2000) to 3.57 m (1997-1998). Inverse relationships were observed between fecal coliform levels and salinity (r(2) = 0.74; P = 0.001) and water temperature (r(2) = 0.69; P=0.001), whereas positive relationships were obtained with total rainfall (r(2) = 0.52; P = 0.013) and Pearl River stage (r(2) = 0.90; P = 0.0001). These relationships are useful for evaluating the potential effects of climate change on water quality and classification of shellfish growing waters in order to protect humans from consuming contaminated shellfish in shallow river-influenced estuaries.