The Phromhot Canal is the only natural water source for consumption and agriculture the Sa Kaeo special economic zone, Thailand. At present, the Phromhot Canal is facing a serious problem with water quality. Our study carried out to analyze and assess the pollution carrying capacity of the natural water resource. The sampling sites were examined 7 stations cut across the downstream areas. All these stations were served as the control station to represent the actual condition of the Phromhot Canal. The results indicated that the water quality of the Phromhot Canal after flowing through the Aranyaprathet Municipality's wastewater treatment plant (AM's-WWTP) was severely contaminated. Effluents from the AM's-WWTP does not meet the effluent quality standard of the Ministry of Natural Resources and Environment, Thailand. In addition, it can flow into the water body up to 6,439.55 m3/day. The maximum amount of a pollutant (in terms of BOD loading) allowed to enter a water body of the Phromhot Canal should be ≤ 0.08 kgBOD/day (dry period) and 16.52 kgBOD/day (wet period). While the Phromhot Canal has to carry BOD loading up to 51.12 kgBOD/day. For this reason, the Phromhot Canal at after flowing through the WWTP was unable to the pollution carrying capacity. From the field survey, the AM's-WWTP is not suitable for wastewater treatment, which has a capacity of 923.93 m3/day. Therefore, it is necessary to strictly control the drainage of the wastewater from the Aranyaprathet Municipality's wastewater treatment system, both quantitative and geographic.