Contaminated water has a very negative impact on the entire agroecosystem. Surface water is usually polluted through the discharge of pollutants of various origins such as wastewater from industries and households, wastewater from livestock, washing harmful chemicals from the soil into the groundwater, oil spills and more. In this water, there are a variety of harmful and toxic substances, as well as pathogenic microorganisms. The consequences can be disastrous and large-scale. One way of removing unwanted and harmful substances from the wastewater is biological. Biological control meansseparation of harmful substances through the metabolism of microorganisms. The aim of this work was to estimate the microbiological quality of water in the canal Danube-Tisa-Danube (DTD) at two differant locations and the possibility of using this water in agricultural production. Water samples for microbiological analysis were taken from one locality near the village Čelarevo, and two lokalities near Vrbas, outside of direct influence of wastewater flows and its tributaries. Water samples were taken according to the guidelines for taking samples of surface water from rivers and streams ISO 5667-6. Time up period was from January to June 2013. Each sample containing 100ml of water was transferred in the laboratory. Microbiological analysis included the determination of total number of bacteria, the number of Salmonella sp., Echerichia coli and the number of sulphite reducing clostridia (genus Clostridia). Large number of saprophytic bacteria as well as the fluorescent Pseudomonas sp. were found at both lokalities in the investigated time period. The number of Salmonella spp. and E. coli was high indicating the presence of water pollution. Sulphite reducing clostridia were recorded in small numbers, only at the end of the test period, which points to a lack of anaerobic conditions in the canal water. The presented results suggest that the water from the tested localities need to be treated before it is used in agricultural purpose.