Habitat suitability models are being widely used for the simulation, under different spatial and temporal scales, of the instream habitat availability for aquatic and riparian species or communities. Their great potential can be also exploited for designing natural like fish-passes in the implementation of the so-called "ecohydraulic trinity": environmental flows (e-flows) assessment, re-establishing river continuity and designing river restoration measures. Indeed, nature-like fish passes can provide both e-flow releases and suitable habitat not only for fish, but for the entire aquatic community. We discuss from a theoretical point of view the potential of the integrated application of these modelling tools with particular regard to the microhabitat and mesohabitat scale approaches (e.g., PHABSIM, Bovee et al., 1982, MesoHABSIM, Parasie wicz et al., 2013). Advantages and limitations of each approach are highlighted and the application domain of each modeling approach is assessed. Results show, on the one hand, the advantages of the mesohabitat scale when channel slope and morphological complexity increase. Whereas, on the other hand, the microhabitat scale demonstrates effectiveness to evaluate potential habitat for motionless organisms, such as, freshwater pearl mussels. Limitations are related to the application of established hydraulic simulation models in the case of coarse substrate, limited water depth and gradient higher than 2%.