Abstract: Improvement of water environmental quality in inland river networks can usually be achieved by water replacement. For a network of constant inflows, optimization of its flow diversion has been one of the approaches to implementation of water replacement in its different branches. Due to the close morphological relation between flow diversion and geometrical characteristics of the channel, a special master-slave relationship of the channel cross section and longitudinal profile versus the discharge of the river network will be developed. In this paper, geometrical characteristics are considered as slave variables, such as the river length l, slope bottom i and bifurcation angle α, and their different weights in prediction of the discharge in each network branch were obtained using fuzzy comprehensive evaluation (FCE) based on the fuzzy theory and rough set theory. To verify this method, a FCE model was successfully applied to a hydrodynamic environment study for the inland river diversion project of Fuzhou. The results are helpful in planning water distribution and scheduling operation schemes for the river network.