The development of aquaculture in An Giang province posed a risk of lowering the surface water quality of the Mekong River. This study assessed the pollution level of surface water affected by aquaculture areas in the province and the efficiency of the floating raft of native aquatic plants on aquaculture wastewater quality improvement. Water samples were analyzed for SS, COD, BOD5, N-NH4+, Total N, and Total P. The Water Quality Index was calculated according to the Vietnamese technical guidelines (VN_WQI). The quadrat method was applied to determine the density of aquatic plants. The result showed that surface water quality affected by aquaculture areas in An Giang province did not meet national standards, and the WQI ranged from heavy to good pollution. Experimental results showed that when using the treatment tank, including floating rafts of Water hyacinth (Eichhornia crassipes), Morning glory plants (Ipomoea aquatica), and Climbing dayflower (Commelina diffusa), the removal percentages of SS, COD, BOD5, N-NH4+, Total N, and Total P were 92.6%, 89.6%, 93.9%, 93.4%, 64.3%, and 94.6%, respectively, in the first three months of the farming season. The removal percentages of SS, COD, BOD5, N-NH4+, Total N, and Total P were 92.7%, 89.9%, 91.5%, 93.6%, 67.8%, and 94%, respectively, in the fourth month until fish harvest in the treatment tank. Therefore, floating rafts of native aquatic plants could absorb nutrients and quickly remove pollutants. The quality of aquaculture wastewater after treatment was significantly improved.