Phragmites australis, as a wide-ranging perennial aquatic plant, is wildly spread in the worldwide. Phragmites australis has adapted to adverse terrestrial habitats such as saline meadow and heavy metal pollution, which makes it become a model species for studying plant environmental adaptability, and has become a research hotspot in the fields of botany and ecology, gradually. A large number of Phragmites australis had been planted in natural and artificial wetlands in Beijing used for removing water pollution. However, the mechanism of monitoring water quality by Phragmites australis has not been clearly studied. In this study, we investigated 8 major water quality indexes of 32 sampling sites distributed all over the major water systems in Beijing and Baiyangdian of Hebei. According to "China National Surface Water Environmental Quality Standard GB3838-2002", the 8 major water quality indexes include pH, dissolved oxygen (DO), total nitrogen (TN), ammonia nitrogen (NH₃-N), total phosphorus (TP), biological oxygen demand (BOD), chemical oxygen demand (COD) and permanganate index (COD_Mn). The results showed that the pollution of 32 water samples were relatively severe. While, the contamination of 32 sampling water were able to be degraded by using microorganism. In addition, the water quality of sampling sites was slightly alkaline, and had the characteristics of high nitrogen (N), high phosphorus (P), high BOD and COD, which indicated that the contamination of sampling sites was extremely serious, and the major pollutants in water are TN and BOD. Principal component analysis (PCA) showed that the 8 water quality indexes could be divided into 3 dimensions, the first dimension was COD/BOD/COD_Mn; the second dimension was TN/NH₃-N/TP; and the third dimension was pH/DO. The water quality indexes within each dimension had a high positive correlation. We further screened out 247 transcripts associated with water quality indexes (Pearson correlation coefficient, PCC ≥ ±0.55) using Phragmites australis transcriptome data (RNA-seq data). Among them, most transcripts (93.9%) were positively correlated with the water quality indexes. The proteins encoded by 132 genes of Phragmites australis related to nitrogen and phosphorus pollution are mainly involved in photosynthesis and protein quality control systems, including protein folding, sorting and degradation; there are also proteins involved in transcription, as well as plant defense systems, signal transduction and lipid metabolism. In addition, there are a large number of unknown proteins. The proteins encoded by 89 genes of Phragmites australis related to organic matter pollution are mainly involved in protein synthesis process and the expression of detoxification genes for degradation of pollutants efficiently. Moreover, it was found that genes transcription and defense system were also response to organic matter pollution. In addition, there are a large number of unknown functional proteins involved. The combination of two genes, PB.4621.1 (encoding GMP synthase) and PB.12079.1 (encoding LEA14 protein), is expected to become a core member of genes for monitoring water quality (N and P levels). Overall, we analyzed the transcriptome changes of Phragmites australis leaves, in order to obtain monitoring genes that can reflect water quality, and to explore new ecological uses of Phragmites australis. This study laid the foundation for the subsequent development of monitoring technology for water quality by using Phragmites australis.