River ecosystems have witnessed a long history of human pressure, particularly the disruption of freshwater fish populations. The awareness of this situation has led to many habitat improvement projects, with a variable degree of success. In natural situations, fish populations co-inhabit throughout the hydrological cycle with different degrees of adequacy, and the sequence of favourable and unfavourable conditions dictates abiotic constraints and biotic interactions that shape the final biological assemblages. We postulate that a part of unsuccessful restoration results is related to insufficient closeness to the natural habitat conditions of the river type that is to be restored, including the naturally adverse periods. We used the river2d model to predict habitat availability as weighted usable area (WUA) at a degraded site that is to be restored, for two native Mediterranean species and their life stages—the Southwestern nase Iberochondrostoma almacai and the Arade chub Squalius aradensis. We then analysed the yearly evolution of the natural WUA at a nearby reference site. Overall, the reference site exhibited the longest periods during which the WUA was continuously lower than the chosen WUA thresholds for each of the four bioperiods. Considerable divergences from natural habitat availability values can be seen for the spawning, rearing and growth bioperiods. Restoration outcomes can result in appreciable deviations—favourable or unfavourable to fish populations—from the WUA occurring under natural conditions over the course of the year. Restoration should therefore take account of local hydraulic and habitat patterns that govern population dynamics and result in the final fish assemblage. Copyright © 2011 John Wiley & Sons, Ltd.