Biodegradation of glyphosate (GLP) and its metabolite aminomethylphosphonic acid (AMPA) was numerically assessed for a vineyard and a wheat field in the Po Valley, Italy. Calculation of the Hazard Quotient suggested that GLP and AMPA can pose a risk of aquifer contamination in the top 1.5 m depth within 50 years of GLP use. Numerical results relative to soil GLP and AMPA concentrations, and GLP age, half life, and turnover time show that GLP was equivalently removed through hydrolysis and oxidation, but the latter produced AMPA. Biodegradation processes in the root zone removed more than 90% of applied GLP and more than 23% of the produced AMPA between two consecutive applications. Doubling organic carbon availability enhanced GLP and AMPA biodegradation, especially GLP hydrolysis to sarcosine. This work highlights that GLP and AMPA removal is controlled by soil water dynamics that depend on ecohydrological boundary conditions, and by carbon sources availability to biodegraders.