When bacterial pathogens from livestock contaminate drinking water supplies, they can cause different forms of gastroenteritis. The objective of this study was to enumerate the concentrations of fecal indicator (Escherichia coli and enterococci) in surface water in order to determine removal efficiency by sand filtration. The concentrations of different indicator bacterial species were determined after running tertiary treated water through two tanks containing aquifer material. Enterococcus faecalis primers targeting the ddl gene and primers for Enterococcus faecium were used to identify the two species in the samples. A PCR assay based on the partial sequence of the 13-D-glucoronidase gene (uidA) for specific detection and differentiation of E. coli populations was used to confirm the presence of E. coli after a biochemical test. The biochemical test overestimated the percentage of E. faecium in our samples, but the PCR assay with the ddl gene produced 100% specificity with Enterococcus faecalis. The biochemical test was 91.5% specific in identifying E. coli. The composition of indicator bacteria in Santa Ana River was dominated by intestinal microflora of humans and animals; filtration by aquifer sand material may reduce the transport of indicator bacteria from surface water to groundwater.