Advances in aquatic ecology can be broadly separated into two contrasting approaches, synthetic vs. incremental. Synthesists study rivers at a holistic level and typically describe important processes in relative terms from headwater to river mouth or across regions. Incrementalists typically quantify relationships of stream flow quantity and quality to fisheries response and are often constrained by institutional requirements. The two approaches can be reconciled using the concept of the habitat template and creation of the Virtual River Reference model. This model should build upon the fundamental principles of natural processes and habitat simulation, determining the physical habitat characteristics of reference river systems as a function of landscape attributes. This approach would use the habitat requirements of the native fish community to reconstruct a corresponding hydro-morphological template of a reference river. The template of habitat attributes can be employed to compare impacted systems to natural or relatively healthy systems (the reference condition) across broad temporal and spatial scales. The summary attribute set can be adjusted to establish a template describing target conditions which are achievable for managers under current or future circumstances. The Virtual River Reference habitat template will create a simulation platform to investigate natural biophysical processes in riverine ecosystem.