The widespread use of pesticides in agriculture during the last several decades has contaminated soils and different Critical Zone (CZ) compartments, defined as the area extended from the top of the vegetation canopy to the groundwater table, and it integrates interactions of the atmosphere, lithosphere, biosphere, and hydrosphere. However, the long-term fate, storage, and transfer dynamics of persistent pesticides in CZ in a changing world remain poorly understood. In the French West Indies, chlordecone (CLD), a toxic organochlorine insecticide, was extensively applied to banana fields to control banana weevil from 1972 to 1993 after which it was banned. Here, to understand CZ trajectories we apply a retrospective observation based on marine sediment core analyses to monitor long-term CLD transfer, fate, and consequences in Guadeloupe and Martinique islands. Both CLD profiles show synchronous chronologies. We hypothesized that the use of glyphosate, a postemergence herbicide, from the late 1990s onward induced CZ modification with an increase in soil erosion and led to the release of the stable CLD stored in the soils of polluted fields. CLD fluxes drastically increased when glyphosate use began, leading to widespread ecosystem contamination. As glyphosate is used globally, ecotoxicological risk management strategies should consider how its application affects persistent pesticide storage in soils, transfer dynamics, and widespread contamination.