Phosphonate‐based herbicides are extensively used in agriculture. Glyphosate was long considered immobile in soils due to strong complexation with metal oxides, but detection in agricultural effluents and surface waters points to glyphosate mobilization and transport. In particular, mechanisms of glyphosate adsorption and subsequent mobility from runoff‐prone soils enriched in quartz have not been fully elucidated. Here we used theoretical and experimental approaches to gain new insights on the soil mobility of glyphosate and two other phosphonate herbicides, glufosinate and fosamine. Molecular modeling simulations of optimized adsorbate complexes of the phosphonate herbicides with quartz and montmorillonite revealed Ca‐enhanced interactions for all three herbicides at both mineral interfaces, weak binding of Na‐complexed phosphonate herbicides on quartz, and more favorable interactions for glufosinate and fosamine with Na‐montmorillonite than for glyphosate. We conducted adsorption and desorption experiments to evaluate the mobility of glyphosate on quartz‐enriched agricultural soils. Consistent with our theoretical findings, adsorption experiments conducted with CaCl2 resulted in greater than a twofold increase in glyphosate retention compared with experiments with NaCl. The desorption experiments revealed release of about 30–90% of the initially bound glyphosate into solution, whereby Ca in the desorption solution promoted glyphosate mobility compared with Na. Furthermore, in all conditions, the relative initial wetness of the agricultural soil was correlated positively with the enhanced glyphosate mobilization, consistent with field‐scale reports that herbicide applied to soils following rain events were prone to runoff.