<p>Biologically secreted carbonates are archives of environmental conditions, as shell and skeletal element minerals record chemical and physical signals of the ambient environment. We report the impact of Cd²⁺ and Pb²⁺ on foraminiferal shell crystal structural and organizational characteristics, such as microstructure, texture, crystal co-orientation strength and crystal twin formation for the rotaliid foraminifera <i>Amphistegina lessonii</i> and <i>Amphistegina lobifera.</i> The investigated species lived first in Cd²⁺- and Pb²⁺-free and, at a later growth stage, in Cd²⁺- and Pb²⁺-containing water. Enrichment in Cd²⁺ was increased 4 times relative to the ecological criteria maximum concentration (CMC) for both species. For Pb²⁺, it was increased 5 times for <i>A. lobifera</i> and 6 times for <i>A. lessonii</i>. Crystal organization was measured with Electron-Backscattered-Diffraction (EBSD), shell structure was imaged with FE-SEM. We detect that the Cd²⁺ and Pb²⁺ concentrations influence the degree of shell calcite twin formation. For <i>A. lessonii</i> the addition of Cd²⁺ to the water prevents crystal twin generation, Pb²⁺ induces decreased twinned calcite secretion. For <i>A. lobifera</i>, both Cd²⁺ and Pb²⁺ significantly decrease crystal twin formation. Our study indicates that crystal twin generation by Rotaliida can be developed as a structural indicator for environmental pollution with heavy toxic elements.</p>