The migration of potentially harmful radionuclides, such as cesium (Cs-137) and strontium (Sr-90), in soil is governed by the chemical and biological reactivity of soil components. Soil organic matter (SOM) that can be modeled through fulvic acid (FA) is known to alter the mobility of radionuclide cations, Cs+ and Sr2+. Shedding light on the possible interaction mechanisms at the atomic level of these two ions with FA is thus vital to explain their transport behavior and for the design of new ligands for the efficient extraction of radionuclides. Here we have performed molecular dynamics, metadynamics simulations, and density-functional-theory-based calculations to understand the binding mechanism of Sr2+ and Cs+ cations with FA. Our studies predict that interaction of Cs+ to FA is very weak as compared with Sr2+. While the water-FA interaction is largely responsible for the weak binding of Cs+ to FA, leading to the outer sphere complexation of the ion with FA, the interaction between Sr2+ and FA is stronger and thus can surpass the existing secondary nonbonding interaction between coordinated waters and FA, leading to inner sphere complexation of the ion with FA. We also find that entropy plays a dominant role for Cs+ binding to FA, whereas Sr2+ binding is an enthalpy-driven process. Our predicted results are found to be in excellent agreement with the available experimental data on complexation of Cs+ and Sr2+ with SOM.