In the area of Kopački rit, in the channel of Čonakut and in lake Sakadaš as well as in the Danube river, the physical and chemical parameters as well as the count of coliform bacteria and E.coli have been studied in the period from March to October 2012. Water quality and floods are one of the most important functions of the ecosystem and are used in the monitoring of the ecosystem services. As coliform bacteria are excreted naturally in a large amount, they are used as an indicator of fecal contamination as well as an indicator of the quality of surface water. By studying the dynamics of coliform bacteria and E.coli between the Danube river and Kopački rit and by determining the variations in the count of coliform bacteria and E.coli in dependence to the distance from the Danube river, it was shown that the number of bacteria decreases from the Danube river towards the borderland of the flooded area. Based on the microbial indicators, in this case the coliform bacteria, the Danube river and the channel of Čonakut belong to the category II type of waters, whereas lake Sakadaš is category I. During the study period, the highest water level of the Danube river was registered in July (454 cm) when 90% of the Kopački rit area was flooded. During the period of floods the count of coliform bacteria and E.coli increased abruptly due to the fact that the hodrological connection of the river and the flooded area as well as several abiotic parameters have an effect on the activity and transport of the bacteria.