<p>Driven by rapid technological advancements and economic growth, mineral extraction and metal refining have increased dramatically, generating huge volumes of tailings and mine waste (TMWs). Investigating the morphological fractions of heavy metals and metalloids (HMMs) in TMWs is key to evaluating their leaching potential into the environment; however, traditional experiments are time-consuming and labor-intensive. In this study, 10 machine learning (ML) algorithms were used and compared for rapidly predicting the morphological fractions of HMMs in TMWs. A dataset comprising 2376 data points was used, with mineral composition, elemental properties, and total concentration used as inputs and concentration of morphological fraction used as output. After grid search optimization, the extra tree model performed the best, achieving coefficient of determination (<i>R</i>²) of 0.946 and 0.942 on the validation and test sets, respectively. Electronegativity was found to have the greatest impact on the morphological fraction. The models’ performance was enhanced by applying an ensemble method to the top three optimal ML models, including gradient boosting decision tree, extra trees and categorical boosting. Overall, the proposed framework can accurately predict the concentrations of different morphological fractions of HMMs in TMWs. This approach can minimize detection time, aid in the safe management and recovery of TMWs.</p>