Based on four seasons of monitoring phytoplankton communities and 9 water quality variables-total nitrogen (TN), total phosphorus (TP), chlorophyll a, chemical oxygen demand (COD), biological oxygen demand (BOD), dissolved oxygen (DO), secchi depth (SD), pH and water temperature (T) at three observatory sites, the water quality of Danjiangkou Reservoir was evaluated using Analytic Hierarchy Process (AHP). The biological diversity index showed the reservoir to be mesotrophic The water quality variables showed that the reservoir belonged to grade III according to the Environmental Quality Standard for Surface Water (GB3838-2002) of China, which suggested the reservoir status could be regarded as lightly polluted. AHP evaluation showed that the water quality was different between the three sample sites, of which the middle reservoir site was the cleanest site (pollution index =0.3619) and the upper reservoir site was the worst (pollution index =0.7755). This study indicates that more attention is required for the upstream pollution of the Danjiangkou Reservoir, and that AHP is a useful tool for water quality evaluation in surface water bodies such as Danjiangkou Reservoir.