The European Union has introduced a new bathing water directive where future classification of recreational waters will be based on the microbial parameters Escherichia coli, and intestinal enterococci. Introduction of enterococci as a new quality parameter may pose a challenge in some areas because relatively less is known about these organisms compared to E. coli. In the present study, the relative abundance of intestinal enterococci, E. coli, and ten fecal sterol and stanol biomarkers were investigated in water and sediment at two estuarine beach sites affected by fecal pollution. In the bathing water, enterococci were relatively more abundant at low E. coli concentrations. In the sediment, enterococci were generally more abundant than E. coli with surface concentrations between 1.0 × 10² and 4.5 × 10³ CFU cm⁻³. Enterococci populations were relatively similar in water and sediment, and were phenotypically different from that of nearby pollution sources. The putative human specific genetic marker esp in Enterococcus faecium was not detected in water or sediment samples despite occasional inputs of human waste from storm water overflows. Sterol and stanol profiles suggested a direct link between water and sediment pollution profiles on days with wind conditions that facilitated resuspension. Sediment resuspension may occur at wind speeds exceeding 6–8 m s⁻¹, and could contribute significantly to enterococci concentrations in the overlying water. The study emphasized that recontamination of the water column due to wind induced resuspension should be considered when evaluating indicator levels and microbial hazards in estuarine recreational waters.