Chlordecone, applied on soils until 1993 to control banana weevil, has polluted water resources in the French West Indies for more than 40 years. At the watershed scale, chlordecone applications were not homogenous, generating a spatial heterogeneity of the pollution. The roles of climate, hydrology, soil, agronomy, and geology on watershed functioning generate a temporal heterogeneity of the pollution. This study questions the interactions between practices and the environment that induce such variability. We analyzed hydrological and water pollution datasets from a 2-year monitoring program on the Galion watershed in Martinique (French West Indies). We conjointly analyzed (i) weekly chlordecone (CLD) concentration monitored on 3 river sampling sites, (ii) aquifer piezometric dynamics and pollutions, and (iii) agricultural practices on polluted soils. Our results showed that chlordecone pollution in surface waters are characterized by annual trends and infra-annual variations. Aquifers showed CLD concentration 10 times higher than surface water, with CLD concentration peaks during recharge events. We showed strong interactions between rainfall events and practices on CLD pollution requiring a systemic management approach, in particular during post-cyclonic periods. Small sub-watershed with high CLD pollution appeared to be a substantial contributor to CLD mass transfers to the marine environment via rivers and should therefore receive priority management. We suggest increasing stable organic matter return to soil as well as external input of organic matter to reduce CLD transfers to water. We identified hydrological conditions—notably drying periods—and tillage as the most influential factors on CLD leaching. In particular, tillage acts on 3 processes that increases CLD leaching: organic matter degradation, modification of water paths in soil, and allophane clay degradation.