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Abstract In human society, there is a demand for sustainable solutions for water preservation and efficient treatment systems. An important water reservoir is road runoff defined as rainwater leaching from roads, loading micropollutants and infiltrating the soil. We aimed to study this poorly understood feature using large-scale metabolomic analysis coupled with analysis of soil physico-chemical properties and molecular chemical similarity enrichment. A total of 2406 micropollutants were assayed to understand their distribution and assess the trapping abilities of a road runoff infiltration system composed of a sedimentation pond and an infiltration pond. Here, we confirm the essential role of the infiltration pond in preventing environmental contamination and propose a model correlating micropollutant abundance and the soil physico-chemical properties. We demonstrate that sand in infiltration ponds is a key player, helping retain 86% of the micropollutant abundance and propose a model that could be easily applied for road runoff management.