Coupling physical and geochemical processes within one integrated numerical simulator provides a process-based tool for investigating the mobility of contaminants as affected by changing hydrologic regimes and geochemical conditions. We review interactions between physical and biogeochemical processes in the vadose zone, and then present a case study demonstrating these complex interactions. A hypothetical application is presented of the HP1 multicomponent transport simulator to predict the transport of two major elements (Ca and P) and one trace element (U) applied annually for 200 yr to a field soil in the form of an inorganic P fertilizer. Interactions of Ca, P, and U with the solid phase are described using cation exchange and surface complexation reactions. Simulations assuming steady-state or transient flow conditions were analyzed in terms of temporal variations of the linear distribution coefficient, Kd, which depends strongly on pH and the composition of the aqueous phase. If the composition of the aqueous phase is constant, adsorption of Ca and U increases with increasing pH. Due to the annual addition of Ca, P, and U, and competition between P and U for sorption sites, the Kd of these elements decreased with time near the soil surface. Deeper in the soil, the Kd of U followed the pH increase because of a lack of competition from P. Because of the combined effects of changing hydrologic and geochemical conditions, the Ca and U distribution coefficients and solute fluxes during the transient simulation exhibited large short-time variations of up to three orders of magnitude.