The theory of water footprints is introduced into the conflict of water and sewage pollution between the upstream and the downstream of a basin, and by using blue and grey water footprints to represent the demand for water utilization and pollution discharge in the regional socio-economic development, the sustainability of the blue and grey water footprints is further obtained to represent the carrying status of water environment in the basin. Finally, based on the theory of rough sets, the overall conflict situation of water utilization and pollution discharge in the basin and the level of conflicts between upstream and downstream regions are quantified as the basis for the future planning of water resources and environment of the basin. Taking the Huangshui River Basin in Qinghai Province as an example, the proposed method is applied to its conflict assessment. The results show that the overall conflict situation of water environment in the basin during the period from 2011 to 2015 is moderate and the trend is relatively stable, and there is a serious conflict in the drought year(2013)of water resources. The conflict between the urban district of Xining City in the downstream and other regions in the upstream and middle reaches is more conspicuous, which needs to be highlighted in the basin planning in the future.