In order to establish a more accurate response relationship between water quality target management of non-point source inputting lakes and reservoirs and total pollution load control in the river basin, a detailed analysis method of dynamic water environment capacity of lakes and reservoirs based on mass balance was proposed with reference to total maximum daily loads, including pollution mixing zone setting, representative hydrological series selection,and daily 2D water quality calculation, with consideration of the influence factors, including runoff variation, inhomogeneous mixing, atmospheric deposition, etc. The Shahe Reservoir in the western hilly area of the Taihu Lake Basin was used as a case study. The dynamic water environment capacity of total nitrogen (TN) was analyzed with the level-Ⅱ water quality for the whole lake and the main lake area, respectively, by using the representative hydrological series from 2010 to 2015. The results show that the annual average values of TN water environment capacity are 36.7 t and 99.43 t under the level-Ⅱ water quality for the whole lake and the main lake area, respectively; if the lakeside mixing zone is not considered, the calculation result of annual TN water environment capacity increases by 66.43%; the larger the area of the water area where the water quality target management is implemented, the greater the influence of atmospheric deposition on the water environment capacity; the inter-annual and intra-annual variations of runoff have significant impact on the water environment capacity; and the ratio of total TN control of each subzone to that of the whole river basin is basically consistent with the area ratio. The method can scientifically analyze spatial and temporal characteristics of the water environment capacity of non-point source inputting lakes and reservoirs, and the results could better support the fine management of the river basin water environment by establishing well link between water quality target management and spatial control of total pollution loads.