Abstract The sea lamprey (Petromyzon marinus) is an anadromous species that occurs in some large Iberian rivers, such as the Tagus, and their tributaries. The sea lamprey populations of the River Tagus are threatened by habitat loss and overexploitation, which means that conservation measures, including maintenance of the spawning grounds, are urgent. Habitat loss is mainly due to hydroelectric and flood‐control dams that have affected the migration and spawning habitats of anadromous species. The main objective of this study was to use a simple, cost‐effective method to assess a minimum instream flow for the regulated River Tagus. The method used was based on the wetted perimeter–discharge relationship, but accounted for the habitat requirements of spawning sea lampreys. In 1998, a habitat survey was conducted along a 30 km segment of the River Tagus downstream from Belver Dam (the first impassable obstacle for fish movements), a stretch that includes potential habitats for spawning sea lampreys. Four spawning areas were identified, and in each one a representative reach was selected along which to collect elevation and geo‐positional data. For a range of flows from 0 to 50 m3 s−1, hydraulic modelling and studies of spawning habitat availability were conducted, both for each reach and for the total wetted area of the four reaches. The availability of spawning habitat was limited by flow. Results showed that the present minimum flow downstream from Belver Dam (8 m3 s−1) is insufficient to ensure suitable habitat conditions in a significant part of the segment studied; gains in wetted usable area were more substantial with discharges of up to 20 m3 s−1, and thus a minimum flow of 10–20 m3 s−1 was recommended. Potential spawning habitat could be improved by increasing instream flow to at least 50 m3 s−1. The impacts of the Belver release regime on anadromous species are discussed and a more ‘ecologically oriented’ form of water management is suggested . Copyright © 2004 John Wiley & Sons, Ltd.