Water soluble chemicals used in agriculture often do end up in the water table. This is part of a process called fate and transport. It follows that water is more of a mechanism of transport, and the chemicals eventually end up somewhere else, be it in sediment or in the tissues of animals that inhabit the water source.
Depending on the type of chemical. Some of them do disintegrate and form other compounds that may be more harmful or harmless. There are some chemicals that persist in water anyway.
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