Groundwater aquifers worldwide experience unsustainable depletion, compounded by population growth, economic development, and climate forcing. Managed aquifer recharge provides one tool to alleviate flood risk and replenish groundwater. However, concerns grow that intentional flooding of farmland for groundwater recharge, a practice known as Ag-MAR, may increase the leaching of pesticides and other chemicals into groundwater. This study employs a physically based unsaturated flow model to determine the fate and transport of residues of four pesticide in three vadose zone profiles characterized by differing fractions of sand (41 %, 61 %, and 84 %) in California's Central Valley. Here, we show that the complex heterogeneity of alternating coarse and fine-grain hydrogeologic units controls the transit times of pesticides and their adsorption and degradation rates. Unsaturated zones that contain a higher fraction of sand are more prone to support preferential flow, higher recharge rates (+8 %), and faster (42 %) water flow and pesticide transport, more flooding-induced pesticide leaching (about 22 %), as well as more salt leaching correlating with increased risks of groundwater contamination. Interestingly, considering preferential flow predicted higher degradation and retention rates despite shorter travel times, attributed to the trapping of pesticides in immobile zones where they degrade more effectively. The findings underscore the importance of considering soil texture and structure in Ag-MAR practices to minimize environmental risks while enhancing groundwater recharge. The study also highlights that selecting less mobile pesticides can reduce leaching risks in sandy areas.