Amazonian fishes employ diverse migratory strategies, but the details of these behaviours remain poorly studied despite numerous environmental threats and heavy commercial exploitation of many species. Otolith microchemistry offers a practical, cost-effective means of studying fish life history in such a system. This study employed a multi-method, multi-elemental approach to elucidate the migrations of five Amazonian fishes: two ‘sedentary’ species (Arapaima sp. and Plagioscion squamosissimus), one ‘floodplain migrant’ (Prochilodus nigricans) and two long-distance migratory catfishes (Brachyplatystoma rousseauxii and B. filamentosum). The Sr : Ca and Zn : Ca patterns in Arapaima were consistent with its previously observed sedentary life history, whereas Sr : Ca and Mn : Ca indicated that Plagioscion may migrate among multiple, chemically distinct environments during different life-history stages. Mn : Ca was found to be potentially useful as a marker for identifying Prochilodus's transition from its nursery habitats into black water. Sr : Ca and Ba : Ca suggested that B. rousseauxii resided in the Amazon estuary for the first 1.5–2 years of life, shown by the simultaneous increase/decrease of otolith Sr : Ca/Ba : Ca, respectively. Our results further suggested that B. filamentosum did not enter the estuary during its life history. These results introduce what should be a productive line of research desperately needed to better understand the migrations of these unique and imperilled fishes.