Anthropogenic factors have been identified as major stressors of nearshore environments such as estuaries, sea grass meadows and mangroves. We hypothesize that aquatic organisms functionally dependent on these habitats as nurseries respond to disturbances with subtle changes in their habitat-use patterns. We used a novel approach coupling behavioural change point analysis with fish otolith microchemistry to analyse continuous life history information independent of climate and physiological variability. Here we show that pre-industrial (1430–1640 CE) land use and fishing practices had little influence on the well synchronized migration behaviour of juvenile snapper Chrysophrys auratus in the Hauraki Gulf, New Zealand. In contrast, modern human disturbances have resulted in snapper spending less time in brackish nurseries and moving chaotically between habitats. Today, nearshore habitats have largely lost their nursery function for the species. Temporal comparison of habitat-use patterns is a powerful tool to evaluate past and present nursery habitat quality.