Based on a whole river network model of Taihu Lake Basin, a nested local mathematical model of water environment was established, calibrated by data from the 31 existed monitoring sites in trans-boundary regions of Jiangsu, Zhejiang and Shanghai. Flux of pollutants, flux threshold and excessive flux value methods for calculating water pollutants in trans-boundary regions were proposed, combined with real-time verification and the domain superposition technique. Subsequently, a water pollutants flux monitoring system for trans-boundary regions of Jiangsu, Zhejiang and Shanghai was developed, in which the primarily operational application was carried out.