Hydrological and morphological characteristics of streams and rivers influence a wide array of ecological processes and patterns; they define the aquatic habitat template. Interdisciplinary approaches are required to study physical-biological interactions; increased collaboration between ecologists and experts in morphology, hydrology and hydraulic engineering is particularly desirable. In this paper, we present our experience of aquatic habitat modelling. In particular, we indicate how statistical instead of mechanistic hydraulic descriptions simplify the input field data required to estimate instream habitat suitability. We have also conducted significant biological validations of habitat model predictions expressed at the fish community level. A better quantification of instream habitat suitability is meaningful when associated with the understanding of the large-scale processes governing stream equilibrium. In this context, the knowledge of bankfull discharge, at which the self-maintenance of the river morphology occurs, is of particular importance. The identification of key hydraulic variables and periods for population dynamics and vital processes are challenging for the near future. A greater understanding of physical-biological interactions will not only yield deeper insights into the ecological organization of streams and rivers, it will also improve our ability to predict how flow alterations caused by various human activities affect these vital ecosystems. Our progresses depend mainly on of our ability to produce biologically validated models.