The state-of-the-art in habitat modelling in the context of minimum flow requirements in Spanish rivers is presented. During the last decade Spanish Water Authorities, by law, had to include evaluations of ’ecological flows’ (considered as minimum instream flows) in their water planning. Most of the ’ecological flows’ determinations have been based on historical flow records (10% mean annual flow or flow frequency distribution) with no serious limnological considerations. However, as environmental awareness increased, Spanish Water Authorities and natural conservation institutions have promoted studies on instream flows based on different methodologies. Palau and Alcazar (1996) proposed a method based on the application of the simple moving average forecasting model as a tool to obtain the information of minimum flows from historical daily flow records. In the Basque country, Docampo and de Bikuña (1995) developed a peculiar method based on the hypothesis that macro-invertebrate communities change along the river continuum. For each watershed, they have elaborated empirical relationships between the number of benthic species, the channel wetted perimeter and the instream flow, and it is assumed that the minimum acceptable flow is the one that is able to maintain at least 15 different species. Our laboratory has been working on flow requirements in streams and rivers based on habitat modelling through Instream Flow Incremental Methodology (IFIM). More than 100 stream reaches in Spain have been studied, analysing bed topography, hydraulic, substrate and refuge conditions, natural flow regime and aquatic communities composition, phenology and habitat requirements. Relationships between instream flows and potential useful habitat were established using 1 and 2-D hydraulic models, together with the habitat requirements of key indigenous fish species and macrobenthic diversity. Minimum flows were determined by selecting those flows that produced the greatest rate of habitat change. The evaluation of the potential habitat produced by natural flow regimes was used to understand the life strategy of autochthonous fishes and their flow requirements. Variability of the natural flow regime was found to be the main factor structuring stream types. In torrential Mediterranean streams, basic flows were ecologically nonsense because the stream channel is too large relative to the wetted channel produced by modal flows. Here, fisheries life strategy is migration and, therefore, minimum flows must be calculated at a scale larger than that of stream reach. Minimum flows, natural flow regime and the habitat requirement of native fish species at different scale, are the components used to the proposal of an ’ecological flow regime’ for each river reach.