Akyatan Lagoon, located on the Mediterranean coast of Turkey, is ecologically and economically important due to biological diversity, valuable fish species, water birds, and wildlife resources. The area was declared a wildlife development area in 2005 and a Ramsar area in 1998. We collected water samples from four stations inside the lagoon and drainage channels during April-August in 2008. All the water samples were analyzed for bacteriological parameters such as total coliforms (TC), fecal coliforms (FC), and physical parameters such as temperature, pH, salinity, and dissolved oxygen (DO). In order to determine the number of fecal and total coliform bacteria, the most probable number (MPN) method was used. The objective of this study is to determine the levels of microbiological pollution in Akyatan Lagoon and drainage channels. Furthermore, observation on the impact of microbiological pollution of drainage channels on Akyatan Lagoon was also the another objective. The results indicated that the minimum TC and FC values were enumerated from the samples taken from all stations (2 MPN/100 ml) during May-August in 2008. The maximum TC levels were obtained in April and June (46,000 MPN/100 ml), while the maximum FC levels were determined in April (24,000 MPN/100 ml) in the S-3 (YD3 drainage channel). Moreover, the relationships between the TC and FC and physical parameters were also assessed, but no significant relationships were observed between the fecal indicator bacteria and environmental parameters. The only relationship that was significant for the TC was with salinity. According to the results, it can be said that there is total and fecal pollution in the two drainage channels flowing in the lagoon, while the lowest TC and FC results were detected inside the lagoon. The seal fishery (S-2) was polluted in terms of TC and FC. There is a potential risk related to the lagoon pollution for people and aquatic life for various activities such as rain, industrial, and urban runoff through drainage channels, agricultural irrigation, accommodating bird feces, and fishing activities. For this reason, the elimination of the source of urban and industrial pollution from drainage channels was needed for the sustainability of Akyatan Lagoon.