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The modification of clay minerals by exopolysaccharides (EPS) may significantly increase their adsorption capacity for heavy metals. This study focused on the adsorption of EPS (produced by Rhizobium tropici)-modified montmorillonite (MMT) and kaolinite (KLT) for Cs and Sr and the influence of external factors (pH, sulfate, and phosphate). The characterization of the composites was carried out using X-ray diffraction (XRD), Fourier transform infrared (FTIR), atomic force microscopy (AFM), and scanning electron microscopy/energy-dispersive X-ray analysis. With EPS modification, the adsorption capacity of MMT for Cs and Sr reached 256 and 90.9 mg/g, respectively, which were significantly improved by 53.8 and 54.5% compared to MMT alone, respectively. The adsorption capacity of KLT for Sr improved by 10.7%. KLT did not adsorb Cs either before or after EPS modification. The adsorption isotherms for Sr on MMT, EPS-MMT, KLT, and EPS-KLT as well as Cs on MMT and EPS-MMT were better described with the Freundlich adsorption models, indicating a heterogeneous layered adsorption process. XRD, FTIR, and AFM analysis confirmed the interlayer reaction of Sr/Cs with EPS-MMT. The Sr amounts adsorbed on EPS-MMT composites increased significantly with increasing pH, while the pH influence was not obvious on Cs adsorption but still slightly increased at pH 7 and then dropped at pH 9. In the presence of 50 and 500 mg/L sulfate, the Sr amount absorbed decreased by 12.5, and 29.3%, respectively. On the contrary, there was a significant increase in Cs adsorption by 12.2 and 33.9%, respectively. In the presence of phosphate, a significant increase (64.5%) was observed for Cs adsorption under 50 mg/L phosphate loading, but 500 mg/L phosphate inhibited (65.8%) the adsorption. In contrast, there was no significant change of Sr adsorption under different phosphate concentrations. The current study would provide a new insight for the application of biopolymers in remediation of Sr- and Cs-contaminated areas.