Abstract: In order to understand the status of water environment in the upper and middle reaches of the Pearl River, it was carried out to survey and measure its water quality, mainly upper the Zhaoqing section, during the three periods of March, June and September 2016, which respected the level period, wet season and early dry season of a year. Ten parameters including pH, dissolved oxygen(DO), non-ionic ammonia(NH₃), ammonia nitrogen(NH₄⁺-N), nitrate nitrogen(NO₃^--N), nitrite nitrogen(NO₂^--N), total nitrogen(TN), total phosphorus(TP), secchi depth(SD) and chlorophyll a (Chla) were selected and assessed by limit value, single pollution index and duty ratio. Water quality of each study area was assessed by comprehensive pollution index. The results showed that the main pollutants were nitrogen nutrient, primarily NO₃^--N and TN. The pollution load of these two pollutants were above 90% among the 17 sampling sites in three periods, and the multiple of max ultra standard of TN was 2.72 at Lubuge in September, 2016, and the multiple of max ultra standard of NO₃^--N was 2.13 at Badu in September, 2016. Besides, NH₃, transparency, TP and chlorophyll a were over-standard in many sites. NH₃, transparency and TP were obviously varied with the hydrologic period, and the Chla was mainly over-standard in the level period and early dry season of the river terminal dammed region at Lubuge site. The phosphorus pollution was primarily presented as the Point Source Pollution (PSP) in the upper and middle region of the Pearl River. Basing on water comprehensive pollution index (P_j), the environmental condition of 17 sampling sites was clustered in three groups. P_j values in cluster I, sampling sites being large water flow rate and distant from residential area, were in the range of 1-2, while the corresponding water quality levels were "light pollution" and "lightly exceeded the alert level". P_j values in cluster Ⅱ, sampling sites being higher TN and NO₃^--N content in the whole year, were in the range of 2-3, while the corresponding water quality levels were "moderate pollution" and "moderately exceeded the alert level". Only Shilong and Tenxian sites were grouped in the cluster Ⅲ, and their P_j values were varied more widely ranges during the three investigation periods than the other two groups. The P_j values of cluster Ⅲ was over 3 in the wet season, which showed the water quality levels were "heavy pollution" and "heavily exceeded the alert level"; comparatively, it was in the range of 1-2 in level period and early dry season, which showed the water quality levels were "light pollution" and "lightly exceeded the alert level" in these times. According to this study, it was suggested that:1) ecological regulation should be considered in the upper terminal dammed area in little rainfall periods to reduce the occurrence of algal blooms; 2) in the main flush period of the Pearl River Basin, mainly during May to August of a year, deforestation, land reclamation and fertilization should be reduced, as well as the municipal waste solids and waters near the river should be promptly removed, to prevent the sands being brought to river and polluting the water environment. The study will provide data supports for protecting and managing the water environment of the upper and middle reaches of the Pearl River.