E. coli isolates in surface water and sediment on creeks and channels on the middle Santa Ana River watershed was characterized after a 12 month study. A survey of the creeks and channels revealed the highest abundance of E. coli in sediment compared to surface water. Higher concentrations of E. coli (up to 4.5 x 106 CFU/g of sediment) or (up to 2.3 x 105 CFU/100 ml of water) were observed in the creeks and channels compared to less than 1.6 x 102 in the control sites and effluent from waste water treatment plants. Pulse field gel electrophoresis (PFGE) was used to characterize the genetic diversity of E. coli isolates from the sites. E. coli isolates from the same sampling locations frequently exhibited the same PFGE pattern or were highly similar to each other. However, E. coli isolates from the same sampling sites but from either sediment or surface water were highly different from each other. This study has identified a unique ecological pattern for E. coli survival and persistence in the environment outside their host.