Silicon (Si) is essential for ecosystem health and Earth's climate, yet human activities such as agriculture have significantly disrupted its natural cycle. In a French agricultural catchment, we found that crop harvesting removes most of the Si released from rocks – 1 to 4 times more than the dissolved Si transport downstream by rivers. Using geochemical tools, including Si isotopes and germanium-silicon ratio, we traced Si cycling and highlighted the impact of agriculture on Si exports.