The effects of water transfer project, which caused a series of changes of the environmental factors, on submerged macrophyte communities have not been fully investigated. We addressed this issue by choosing the channel river and impounded lakes of the east route of South-to-North Water Transfer Project (SNWTP) as one case study. Seven natural populations of Potamogeton crispus L. in Beijing-Hangzhou Grand Canal, Lake Gaoyou, Lake Hongze, Lake Luoma, Lake Nansi, and Lake Dongping were investigated to determine the functional traits and their relationships with environmental factors. The results indicated that:(1) total nitrogen (TN), nitrate nitrogen (NO₃-N), ammonia nitrogen (NH₄-N), total phosphorus (TP), orthophosphate (PO₄-P), silicate (SiO₄-Si), chlorophyll a (Chla), total dissolved solids (TDS), transparency (SD), extinction coefficient (K), water temperature (T), conductivity (Cond), pH value (pH), dissolved oxygen (DO), and sediment water content (S_w) differed significantly among the surveyed channel river and impounded lakes except permanganate index (COD_Mn), turbidity (Tur), and sediment organic matter content (S_o). (2) All 18 functional traits, including plant height, branch number, internodes number, internodes length, stem diameter, relative stem length, leaf number, leaf thickness, leaf length, leaf width, leaf area, relative leaf area, plant weight, stem weight, leaf weight, stem leaf ratio, stem dry weight ratio, and leaf dry weight ratio were significantly different among the channel river and impounded lakes. (3) In terms of the coefficient of variation (CV) from low to high, the order of 18 functional traits was leaf width, stem diameter, leaf length, stem dry weight ratio, leaf dry weight ratio, leaf area, plant height, internodes length, relative stem length, stem leaf ratio, leaf thickness, internodes number, stem weight, leaf number, plant weight, relative leaf area, leaf weight, and branch number. Regarding to the mean CV of all functional traits from high to low, the order of 7 channel river and impounded lakes was lower region of Lake Nansi, Lake Hongze and Beijing-Hangzhou Grand Canal, Lake Gaoyou, Lake Dongping, upper region of Lake Nansi, and Lake Luoma. (4) Redundancy analysis (RDA) result showed that 18 environmental factors explained 49.43% of total variation of functional traits. In general, the leaf traits had a significant correlation with nutrient factors (TN、NO₃-N、SiO₄-Si), and the stem traits were closely related to light factors (Chla and SD). While the biomass allocation of stem and leaf was mainly determined by the sediment factor (S_o).