The Hydro-system Danube-Tisa-Danube stretches along 12 700 km2 in the North of Serbia. In view of the multiple role of the canals (drainage, irrigation, water supply of settlements and industry, navigation, fishing, etc.), there are numerous pollution sources that influence the water quality. Using the data of the Republic Hydrometeorological Service of Serbia, the paper analyzed the water pollution levels in the canals using the combined physical-chemical WPI index (water pollution index). The samples were taken monthly from a total of 9 stations between 2004 and 2009. The following parameters were taken into consideration: dissolved O2, O2 saturation, pH, suspended sediments, biological oxygen demand (BOD5), chemical oxygen demand (CODMn), nitrites, ammonium, saprobic index, metals (Fe, Mn, Ni, Hg), sulphates and coliform germs. The mean WPI values are calculated for the respective period based on the comparison of mean annual values of parameters and defined standard values for the I class of water quality (according to the Rules of Procedure on the Hygienic Quality of Water of the Republic of Serbia). The research has shown a decreasing trend in pollution since 2007 as a result of performed canal water cleansing. The analysis of parameters (BOD5, ammonium, coliform germs) that have the greatest impact on the pollution confirmed the prevalence of organic pollution compared to the non-organic one, so that food industry, agriculture and sewage water feature as major polluters.