Water function area compliance evaluation plays a vital role in implementing the strictest water resources management system andwater pollution control. Annual Averaging Method (AAM) and Exceeding Frequency Method (EFM) are the two main methods for waterfunction area compliance evaluation. Water quality data of sixty-four water function areas during 2013-2017 were selected to investigatethe difference between two methods in W district of S city from the plain river network of the Taihu Basin. The results show that regionalcompliance rates of AAM are 18% and 24% higher than those of EFM respectively, based on two factors (CODMn and NH3-N) and threefactors (CODMn, NH3-N, TP). Regional compliance rates of AAM are 11%, 12% and 14% higher than those of EFM for CODMn, NH3-N, TPas being single factor. The number of water function areas with different evaluation results occupy 41% of all of the water function areas.Those water function areas without the same evaluation results are mainly distributed in the area where streamflow is often sluggish andprone to be standstill. Water pollution source and rainfall might be the key factors affecting the assessment results. Comprehensiveconsideration of water quality characteristics, the response of aquatic ecosystem on water quality, historical consistency of evaluationoutcomes and practical management feasibility should be taken carefully when choosing compliance evaluation method.