Spanish Pyrenean streams are characterized by extreme summer drought and torrential flows during spring snowmelt and their fish communities are dominated by trout at high altitudes and by barbel in the lower reaches. The Instream Flow Incremental Methodology (IFIM) was adapted to analyse the fisheries habitat of Spanish streams. Parameters were developed that measure the particular characteristics of these streams, taking into account the habitat needs of the main developmental stages (adults, juveniles, fry and spawning) in different seasons. For this analysis 'potential habitat' was defined as that determined by hydraulics and geomorphological features. 'Real habitat used' was defined by the fish population characteristics (densities, biomass, age-structure and population dynamics). Habitat complexity was calculated as the diversity of habitats of different developmental stages and different species. Habitat conditions during summer-drought were analysed by the simulation of low flow conditions as measured by gauging stations. Habitat parameters were measured in several stream reaches and compared with the characteristics of the fish populations they supported by multivariate analysis. The results show that fish abundance increases downstream along the river continuum, indicating that the habitat carrying capacity increases downstream. The depth and rock surfaces are the main factors limiting the capacity of the stream to provide refuges. Trout populations are also influenced by submerged macrophytes. This IFIM evaluation of stream habitat was not correlated with fisheries features because factors other than hydraulics appear to limit trout population in the Pyrenean study streams. Hydraulic factors may limit the fish populations during brief periods, but population recovery from these disturbances may take longer than the time available between disturbances events.