Dispersal is a critical determinant of animal distribution and population dynamics, and is essential information for management planning. We studied the movement patterns and the influence of habitat and biotic factors on Mediterranean brown trout (Salmo trutta) by mark-recapture methods in three headwater streams of the Ebro Basin (NE Iberian Peninsula). Fish were sampled by electrofishing on five occasions over 18–24 months and movements of over 3,000 individually tagged trout (age 1+ onwards) were recorded. Most of the tagged fish exhibited limited movement and were recaptured within 100 m from the initial capture section. Small seasonal differences in the movement pattern were observed, but in two of the streams, displacement distances increased prior the spawning period in autumn. The frequency distributions of dispersal distances were highly leptokurtic and skewed to the right and fitted well to a two-group exponential model, thus trout populations were composed of mobile and stationary individuals, the latter being the predominant component in the populations (71.1–87.5% of individuals). The mean dispersal distances, for fish captured at least in three sampling events, ranged 20.7–45.4 m for the stationary group and 229.4–540.5 m for the mobile group. Moving brown trout were larger than non-moving individuals and exhibited higher growth rates in two of the streams. Habitat features were not consistently linked to movement rates, but there were some interaction effects between stream and habitat characteristics such as depth, cover and water velocity.