The aim of this study is to find out the density of the fecal bacteria and to analyze resistance to antimicrobials of Gram negative bacilli isolated from the Kucukcekmece Lagoon, Istanbul. Samples were taken monthly from June 2006 to June 2008 and a total of 232 Gram negative bacilli were isolated. Chloramphenicol, tetracycline, nalidixic acid, ampicillin, imipenem, ceftazidime, amikacin, streptomycin and amoxicillin + clavulanic acid were used in antimicrobial susceptibility tests. Susceptibility to trimethoprim + sulfamethoxazole was also examined in only integron-bearing organisms. The antibiotic resistance tests resulted in bacteria being the most resistant against ampicillin (76.29%) and the most sensitive against amikacin (93.56%). Of 232 isolates, 20 (8.6%) coliforms harbored class 1 and/or class 2 integrons. DNA sequencing showed that variable regions of the integrons harbored various gene cassettes; dfrA12, dfrA15, dfrA17, aadA1, aadA2, aadA5, blaOXA-30 and sat2. Integrons were found in bacteria from all sampling areas except 12 and D3. In this study, the determination of bacterial identification of the species of Gram negative bacilli and their Antibiotic Resistance Profiles in the Kucukcekmece Lagoon for the first time was investigated. A finding indicates that there is a heavy fecal pollution in this lagoon environment, which might probably be resulted from the intensive anthropogenic facilities. The risk to public health could be the transfer of antibiotic resistance determinants from the bacterial isolates to normal microbiota bacteria of humans unless the effective precautions such as water treatment plants are taken.