Habitat fragmentation is widely assumed to have negative effects on populations and communities, but some effects of fragmentation are subtle, difficult to measure and not always negative. For stream fish, barriers to upstream passage, such as waterfalls or culverts with perched outlets, are a common cause of fragmentation. We explored the effects of barriers on a virtual stream trout population occupying a network of reaches in the inSTREAM individual-based trout population model. The model includes daily habitat selection by individual fish, with barriers represented by assuming trout cannot move upstream past a barrier and move downstream over a barrier only if habitat above it offers low potential fitness. In 78-year simulations of a resident trout population occupying the stream network of a 25-km2 catchment, we varied barrier density and observed effects on population stability properties and demographics. Increasing barrier density decreased subpopulation persistence in first-order tributaries but not larger streams. Barriers at tributary mouths reduced the population's resistance to extreme flows, but additional barriers caused no further loss of resistance. Barriers reduced overall abundance and biomass at intermediate and high densities and caused a small but surprising increase in biomass at low density. In comparison with fish in the remainder of the network, fish in isolated first-order tributaries had higher survival early in life, smaller sizes at age and reproduced as smaller, younger individuals. Fish that passed over barriers contributed relatively little to downstream populations but, had they not moved, would have increased persistence and abundance of the tributaries they moved from. Relationships such as these would be very difficult to elucidate without a model representing individual behaviour. Copyright © 2011 John Wiley & Sons, Ltd.