The transfer of nutrients and contaminants from bulk soil to roots and into plants depends on many plant and soil processes. The RhizoMath approach for modeling co-occurring processes in the rhizosphere, including speciation in the soil solution, is based on coupling the mathematical package MATLAB with the geochemical code PHREEQC. In addition to the built-in initialization module that performs calibration against experimental data, RhizoMath's greatest advantage is that different geochemical models (with and without charge balance) and geometries (planar and radial) are already included. Moreover, due to its graphical user interface, the tool can be applied without changing the source code or a complex input file. The model was verified using a benchmark and experimental data: (i) the initialization module was successfully applied to describe concentrations measured in soil solution samples; (ii) the theoretical problem “diffusion of K toward a single root” was used to demonstrate that the performance of applied numerical methods is comparable to other approaches; and (iii) for compartment system experiments involving more complex speciation, RhizoMath was able to describe the observed effects of citrate exudates on the simultaneous transport of arsenate and phosphate that compete for surface binding sites with each other and with other oxyanions such as citrate.