Rivers shape the landscape and determine spatial connectivity for a variety of riverine and terrestrial organisms. Rivers impacted by human disturbances are often in need of restoration in order to increase their functionality and ecological diversity, and ultimately to improve the ecosystems services that they offer. Because it is usually assumed that physical diversity of river systems promotes biological diversity or riverine species, river restoration practices often tend to enhance simplified rivers by increasing structural morphological complexity of river reaches. However, the relationship between the variability of physical features and the biological communities in riverine environments is not necessarily straightforward to assume due to the high degree of complexity and feedback in the relationship. This work presents a case study with the application of a recent geomorphological method developed in Europe for the assessment and characterization of geomorphic conditions in combination with biological surveys, along a mountain river basin in Central Chile (Clarillo River).Although representing a single snapshot in the pulsating nature of a river system, our results suggest that availability of habitats provides the conditions to support different levels of biodiversity in a hierarchical way in terms of spatial scale. In particular, we found that abundance and diversity of macroinvertebrates are more related with 2 composition of geomorphic units, whereas the presence of fish is more related with the geomorphic nature of the reaches, and the presence of anurans is more related with the geomorphic nature of river segments.