Amazonian goliath catfishes are widespread in the Amazon Basin. Recently, otolith 87Sr:86Sr analyses using laser ablation–multi‐collector–inductively coupled plasma mass spectrometry (LA‐MC‐ICPMS) revealed a >8,000 km trans‐Amazonian natal homing in Brachyplatystoma rousseauxii among fish caught and hatched in the largest Amazon River tributary, the upper Madeira basin. Although also suspected for fish in the upper Amazon, homing could not be demonstrated owing to less distinct environmental 87Sr:86Sr gradients along the Amazon mainstem. Using scanning X‐ray fluorescence microscopy (SXFM), a separate study provided evidence that Se:Ca and Sr:Ca are useful markers for identifying migration into Andean headwaters and the estuarine environment. We analysed otoliths of known 87Sr:86Sr profiles using SXFM mapping to test if Sr:Ca and Se:Ca patterns could demonstrate natal homing...