Wetland habitats are crucial for many fish species as spawning, feeding or nursery areas, but the major factors that govern their use by fish are poorly identified. In the present study, we aim to investigate the selective use and the spatial distribution of native and non-native fish species in different types of wetland habitats (grasslands and reed beds) in a large freshwater marsh (North Western France). The selective use was measured by comparing the community that uses wetland habitats to the total community of the marsh (sampled in the permanent aquatic habitats (canals) during the low water period). The spatial distribution was studied by analyzing the presence probability of fish in wetland habitats as a function of the distance from adjacent canals. All sampled wetland habitats were occupied by fish, and the fish community in wetland habitats was dominated by three native (Abramis brama, Scardinius erythrophthalmus and Anguilla anguilla) and three non-native (Ameiurus melas, Gambusia holbrooki and Lepomis gibbosus) species. Species richness and total fish abundance differed between canals and wetland habitats as a consequence of a variable propensity to use wetland habitats by native (avoidance and preference) and non-native (no preference) species. Non-native species were also more abundant in reed beds than in grassland while no differences were observed for native species. Universally, the presence probability of fish always decreased in wetland habitats as the distance from the canals increased and only a narrow area, close to canals (50–80 m), was well used by fish. However, non-native fish species used over greater distances in reed beds than in grasslands while no differences were observed for native species. Variable interpretations related to species tolerance, reproductive guilds or diet are proposed to understand the mechanisms that might explain the widespread success of non-native species in this spatially varying environment. Copyright © 2008 John Wiley & Sons, Ltd.