Rivers are among the ecosystems that have been most damaged by human pressure, especially in European countries where most streams are regulated. An important instrument to mitigate such impacts is to provide adequate ecological flows, which allows for the preservation of fish populations. Nowadays, many rivers are invaded by exotic species that, being more opportunistic and tolerant, are changing the global biodiversity by competing with native populations. Therefore, while defining ecological flows regimes or during a restoration project design, the existence of exotic species should be taken into account. A project concerning the establishment of an ecological flow regime was undertaken in the Ocreza River, in the eastern center of Portugal. The Instream Flow Incremental Methodology (IFIM) was applied, using the River2D model, to simulate the hydraulic variables and the fish habitat. Close analysis of the results, in terms of WUA values, supported the development of metrics in order to increase the habitat for native species and, at the same time, decrease the habitat for exotic species.