Rivers are one of the most valuable aquatic ecosystems that their physiochemical properties and the biology of their organisms have strong interactions. One of the major rivers in Iran, which covers a variety of ecosystems, is called Tajan River. In this research, the effect of different pollution sources on water quality of this water body was investigated. Samples were collected in seven different sampling seasons (with three week intervals), which had been selected based on agricultural activities in the study area. The levels of nitrate, nitrite, phosphate, ammonia, dissolved oxygen, hardness, alkalinity, pH and BOD5 were measured. The results showed that the concentrations of phosphate and ammonia were much higher than the global standards for river environments. High levels of alkalinity and hardness observed in this river can be useful for the ecosystem health. The levels of other parameters were within or lower than the global standards. However, BOD5 showed higher levels than these standards in some stations.