Coastal wetlands are receiving increased attention as a putative source of fecal indicator bacteria (FIB) in Southern California coastal waters. We examined temporal trends of water and sediment-associated FIB after rain events along with spatial sediment characteristics at two sites within the Santa Ana River wetlands and made comparisons to FIB levels observed in adjacent surf zone waters. During the first two rain events, total coliforms (TC), Escherichia coli (EC) and enterococci (ENT) in wetland water and sediment samples peaked either on the same day or within several days of the rain event, while the third resulted in elevated wetlands sediment TC levels only. TC in adjacent coastal waters consistently peaked on the same day as the rain event and decreased quickly thereafter (within 1 day). The TC/EC ratios of surf zone samples consistently fell below 10, indicating an increased probability of human fecal contamination whereas wetland TC/EC ratios were higher, averaging approximately 60 and 14 at each site. These results suggest sediment-associated FIB populations may be distinct from those found in the water samples, or at least have internal dynamics independent of water-borne populations. Increases in sediment-associated FIB may be due to in situ population growth and/or increased survival due to changes in environmental parameters (salinity, moisture and nutrient input) resulting from the rain events. Spatial differences in between the two sites may be due to sediment differences such as organic content and finer grain size and/or discrete sources of FIB.