Two fungal species were isolated from the studied rock samples and identified morphologically as Aspergillus hollandicus and Penicillium citrinum. Bioleaching process was applied to W1, W2 and W3. The average concentration activity of 238U, 226Ra, 232Th, and 40K are 5134.03, 5708.64, 189.51, and 1456.8 BqKg−1, respectively. Radionuclide’s distribution in leach liquor, residual, and fungal adsorption were followed and environmental hazard indices (Raeq, Iγ, Hex, Hin, and ECLR) were calculated. From the observed outcomes, the isolated fungal strains have the potential to reduce the harmful effect up to 50% compared to the original. As a result, application of these fungal strains offers a potential strategy for environmental remediation of radionuclides.