Evaluation of microbial water quality is commonly based on monitoring populations of fecal indicator organisms (FIO) such as Escherichia coli (EC) and enterococci (ENT). The occurrence of elevated FIO concentrations in surface waters after storm events is well documented and has been attributed to runoff and sediment resuspension. The reasons for FIO concentration variation under baseflow conditions are less clear. The objective of this study was to quantify the variability of EC and ENT in two small streams running through agricultural land use areas. FIO concentrations were measured at upstream and downstream locations under baseflow conditions. Concentrations were not significantly different along cross-sections of the streams. Diurnal concentration trends were observed at each of the sampling locations. Significant differences in concentrations between upstream and downstream locations were noted for both creeks during baseflow periods when no runoff or sediment resuspension occurred. A hypothetical explanation is that indicator organisms are released from sediments during baseflow conditions due to the effect of groundwater influx into streams or due to the motility of indicator organisms. If confirmed, this hypothesis may affect our understanding of the role of sediments in the microbial quality of surface waters.