Worldwide large rivers continue to be used as water sources for irrigation or hydroelectric power generation and such developments typically have adverse impacts on riverine fish populations. In New Zealand, these large rivers often support important recreational brown trout fisheries but knowledge gaps surrounding trout biology means the consequences of modifying large rivers are not fully understood. To address this issue, we examined the most comprehensive temporal brown trout dataset collected in New Zealand (Glenariffe Stream, upper Rakaia River). Annual fish trap records from 1965–1993 showed an eight-fold variation in the number of spawning trout recorded annually; larger runs consisted of higher proportions of small fish and first-time spawners than did smaller runs. 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 fish of both sexes typically arrived two months later than the initial smaller spawners. Data from fry traps illustrated that water level, month-of-year and lunar phase were the key drivers of juvenile outmigration. Recoveries of tagged fish showed the importance of longitudinal connectivity between spawning tributaries and estuarine habitats, particularly for ‘spent’ females, as these adult fish moved more than 100 km downstream post-spawning to estuarine habitat to rapidly regain condition. Collectively our findings quantify the inherent annual variability in brown trout spawning runs and the catchment-wide scale that brown trout population dynamics occur over. Managers need to comprehend these upstream-downstream linkages when making river-modification decisions.