Green infrastructure (GI) networks comprising multiple natural and artificial habitats are important tools for the management of ecosystem services. However, even though ecosystem services are deeply linked with the state of biodiversity, many approaches to GI network planning do not explicitly consider the ecological needs of biotic communities, which are often threatened by anthropic activities even in presence of protected areas. Here, to contribute in fill this gap, we describe an easy-to-apply, biodiversity-centric approach to model an ecological network as a backbone for a GI network, based on the ecological needs of a range of representative species. For each species, ideal habitats (nodes) were identified, and crossing costs were assigned to other habitat types depending on their compatibility with the species ecology. Corridors linking the nodes were then mapped, minimizing overall habitat crossing costs. We applied the method to the Isonzo–Vipacco river area in Northern Italy, highlighting a potential ecological network where nodes and corridors occupied 27% and 11.8% of the study area, respectively. The prospective of its conflicts with anthropic activities and possible solutions for its implementation was also discussed. Our method could be applied to a variety of situations and geographic contexts, being equally useful for supporting the protection of entire biocenoses or of specific sensitive species, as well as enhancing the ecosystem services they provide.