Nerium oleander L. (Apocynaceae) is a micro-nano phanerophyte that grows in the riverbanks of the Río Tinto basin (Southwest Iberian Peninsula). The waters and soils of the Río Tinto area are highly acidic and have high concentrations of heavy metals. In this environment, N. oleander naturally grows in both extreme acidic (EA) and less extreme acidic (LEA) water courses, excluding, and bioindicating certain metals. In this work, we compared and evaluated the accumulation preferences and capacities, the distribution and processes of biomineralization of metals (Fe, Cu, Zn, Mn, Mg, Ca) in the first stages of growth of EA and LEA oleanders by means of inductively coupled plasma-mass spectrometry, scanning electron microscopy, and energy dispersive X-ray analyzer analysis. Seeds from both environments were grown and treated with a self-made solution simulating the most extreme red waters from the Río Tinto. LEA plants drastically reduces the metal uptake at the beginning, but later reactivates the uptake reaching concentration values in the same range as the EA plants. The results showed high Mn, Zn and Mg concentrations, accumulation of Fe and Cu in plants from both environments, differing from the metal concentrations of field-grown oleanders. Iron bioformations with traces of other metals were present inside and over epidermal cells and inside vascular cells of stems and roots. They were absent of leaves. The accumulation properties of N. oleander in its early stages of development make it a species to take in consideration in phytoremediation processes but optimized conditions are needed to ensure enough biomass production.