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Pesticides can have a number of adverse impacts on crops, soil and water. In this paper, we focus on the physical and hydraulic properties of soils controlling the leaching of pesticides into the shallow groundwater of the Rattaphum Catchment in Thailand. Results from an analysis of soil physical properties, hydraulic conductivity, dye tracer and bromide tests show that the top 10–30 cm of soils in the three agro-ecosystems (vegetables, fruits and rubber) have a high clay and organic carbon content and are relatively impermeable with very low hydraulic conductivity (15–40 cm/day). Most of the dye and bromide were retained in the top clayey layer; the bromide forming a miniature bulge below 30 cm in two profiles which dissipated after 30 days, while the pesticides were mainly confined to the top 10 cm.