<p>The present study was examining the remediation and elimination of Mayer’s Hematoxylin (MHX) solutions, a widely utilized dye in biochemical and biomedical laboratories, via adsorption process onto a naturally occurring clay mineral (NC) explored as a cost-effective and efficient adsorbent. Natural clay (NC) were characterized its properties through SEM, EDX, XRD, BET, FTIR, and TG&amp;DTG techniques to identify active sites and structural characteristics. The treatment of MHX, especially at pH 3.5, presents notable challenges owing to the stability in aqueous solutions. The adsorption isotherms were assessed through Langmuir and the Freundlich isotherm models. The Langmuir model exhibited the superior fit (R² = 0.98) and suggested a maximum adsorption capacity of 17.5 mg g⁻¹. Kinetic studies indicated that the pseudo-first-order model accurately represented the adsorption process, attaining the R² value of (0.98). Batch adsorption experiments confirmed the effectiveness of NC in treating laboratory wastewater containing Mayer’s Hematoxylin. The findings of NC demonstrate the efficacy of palygorskite clay as a sustainable adsorbent for treating medical and laboratory effluents, presenting a viable approach to address environmental and wastewater management issues. The uniqueness of this study is to use natural clay as an adsorbent to eliminate MHX dye. Finally, Natural clay (NC) showed high efficiency in treating real wastewater samples from diagnostic laboratories in health sectors, suggesting a potentially cost-effective and sustainable alternative to conventional treatment methods for medical facility waste management.</p> Graphical abstract <p></p>