Canal 900 is an open lined channel constructed to deliver 30 MCM per year of water from Qaraoun Lake at Litani River to irrigate agricultural lands of Bekaa Valley, Lebanon. From its inception, this canal has been plagued with setbacks due to excessive algal proliferation. This study aims at the assessment of the water quality indicators in 325 water samples of Canal 900 starting from the point of water outlet at Qaraoun reservoir till its end through the 2012 irrigation season. The results indicated elevated nutrient (nitrates and phosphates) concentrations that exceeded the recommendations to prevent aquatic ecosystems from developing eutrophication and algal proliferation all through the canal. This was associated with low DO levels and very high levels of BOD5 and COD. In addition. significant spatial and temporal differences (at p <0.05) in the mean values of most indicators were shown. The finding of this study should be considered in the development of a suitable water quality monitoring program and management strategy of both Qaraoun Lake and Canal 900 for a more safe use by farmers.