The prevalence of faecal coliform bacteria and to detect Escherichia coli via the uidA gene, to identify the associated faecal pollution sources and to predict faecal contamination in an active seaside area of the Marmara Sea. Systematic microbiological testing and PCR/DGGE analysis of subsequent isolates. Most probable number (MPN) analysis was performed to monitor the E. coli population in seawater over a period of 24 months (January 2009-December 2010) and the genetic heterogeneity was determined using uidA PCR/DGGE analysis of subsequent isolates. The prevalence of total coliform bacteria ranged from a mean MPN value of 10¹ -10⁴ per 100 ml. In this study, in addition to E.coli other enteric bacteria species were also detected at Stations 4 and 5. It could be concluded that post bloom waters contain secondary metabolite compounds exhibiting anti-bacterial activity against E.coli. Analysis of uidA gene using BLAST analysis showed a temporal and spatial genetic homogeneity in E. coli marine populations. We concluded that the enteric bacteria levels observed at the stations sampled, are a likely consequence of the discharge of untreated wastewater to the Ayamama Stream and Kucukcekmece Lagoon on the coastal line. It is interesting to note that there were no remedial activities, even though the anthropogenic pollutants were above levels considered a threat to human health. The high density of faecal coliform bacteria and prevalence of E. coli in the area under study suggests a potential public health risk of water-borne outbreaks.