Heavy metals (HMs) are routine contaminants due to their extensive use worldwide. Rare earth elements (REEs) are emerging contaminants because of their global exploitation for use in the high-tech sector. Diffusive gradients in thin films (DGT) are an effective method for measuring the bioavailable component of pollutants. This study represents the first assessment of the mixture toxicity of HMs and REEs in aquatic biota using the DGT technique in sediments. Xincun Lagoon was chosen as the case study site because it has been contaminated by pollutants. Nonmetric multidimensional scaling (NMS) analysis reveals that a wide variety of pollutants (Cd, Pb, Ni, Cu, InHg, Co, Y, La, Ce, Pr, Nd, Sm, Eu, Gd, Dy, Ho, Er, Tm, and Yb) are primarily impacted by sediment characteristics. Appraisal of single HM-REE toxicity reveals that the risk quotient (RQ) values for Y, Yb and Ce notably exceeded 1, demonstrating that the adverse effects of these single HMs and REEs should not be ignored. The combined toxicity of HM-REE mixtures in terms of probabilistic ecological risk assessment shows that the Xincun surface sediments had a medium probability (31.29%) of toxic effects on aquatic biota.