Emission trading is one of the most effective alternatives to controlling water pollution. Water environmental functional zone (WEFZ) is used to determine the water quality standard and identify the zone boundary for each river or reach. In this study, a new emission trading scheme was addressed based on WEFZ, accounting for both the temporal dimension and water quality control. A temporal factor of emission trading was proposed based on variations in the environmental capacity within a year by dividing the year into three periods, including high, normal, and low periods of environmental capacity. During each period, emission trading was implemented exclusively. A water quality-control scheme was suggested based on the water quality requirement in the water functional zone, in which the water quality at the downstream boundary of the zone was required to meet the water standard following auto-purification in the stream. Two methods of calculating water quality control are addressed for point-source pollution and non-point-source pollution. The calculated temporal dimension and water quality control were located in Dongxi River of the Daning Watershed in the Three Gorges Watershed. The high period was during June, July, and August, the normal period was during April, May, September, and October, and the low period was during January, February, March, November, and December. The results from the water quality calculation demonstrated that the discharge of point-source and non-point-source pollutions led to an excess of common contaminants at the downstream boundary of WEFZ. The temporal and spatial factors above should be incorporated into the emission trading scheme based on WEFZ.