In this study, laser ablation–inductively coupled plasma–mass spectrometry was used to characterize the growth patterns of otolith of Micropogonias furnieri from southeastern Brazil under the influence of coastal marine upwelling. Archaeological fish sagittae otoliths of M. furnieri recovered from Brazilian shell mounds (5820‒4980 cal BP) were analysed and compared with those of modern specimens. Otolith Sr/Ca analysis indicated that off southeastern Brazil, M. furnieri shifted from freshwater/brackish in archaeological specimens to brackish/marine in modern times. Regular core-to-edge Sr/Ca oscillations suggest that both modern and archaeological M. furnieri are resident estuarine fish that also use the marine waters adjacent to the coastal zone. Based on analyses of a wide range of otolith edge Sr/Ca values measured in archaeological samples, pre-colonial fishing activities in the coastal regions of Guanabara Bay occurred throughout the year. This study reinforces the importance of M. furnieri as a precolonial fishing resource in this area and demonstrates a shift in fishing practices, where smaller fish are targetted within the bay and larger fish are caught beyond the bay. These data may also be indicative of a shift in the life cycle of this species, possibly caused by the overfishing of this important resource and significant increase in human activities in protected coastal waters in modern times.