Globally, many large rivers are modified to meet human needs, often with adverse impacts on fish populations. In New Zealand, these large rivers often support important recreational brown trout ( Salmo trutta) fisheries but understanding the impacts of flow alterations on connectivity for trout is limited. We analysed the most comprehensive fish trap dataset collected in New Zealand (Glenariffe Stream 1965–1993). Annual brown trout spawning counts varied eight-fold; larger runs had higher proportions of small fish and first-time spawners. Return spawning fish sustained the run for years with smaller runs. There were sex-based differences in the size and timing of fish reaching spawning grounds although the larger males and females typically arrived two months later than initial smaller spawners. Recoveries of tagged trout showed the importance of longitudinal connectivity between spawning tributaries and lagoon habitats with adult females moving >100 km downstream to rapidly regain condition. With inherent annual variability in spawning runs, and the catchment-wide scale that brown trout population dynamics occur over, managers need to understand these upstream–downstream linkages when making river-modification decisions.