Soil organic matter (SOM) can bind to and control the transport of many contaminants. While many studies have shown the importance of SOM and the transport of inorganic contaminants like inorganic metals, the interactions between organic contaminants like neonicotinoid insecticides have received much less attention. This study is the second part of a 2-part series on the Wignell Drain, where we quantified three commonly applied neonicotinoids: imidacloprid, clothianidin and thiamethoxam in agricultural surface soils and stream sediments of an agricultural drain in Southern Ontario between April and September 2023. We also monitored benthic macroinvertebrate community structure, determined the molecular composition of SOM extracts using Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS), and quantified SOM. Imidacloprid concentrations peaked in surface soils in April and May at 5.44 ppb, shortly after planting season. Thiamethoxam and imidacloprid concentrations peaked between June-August, ranging from 1.24-1.56 ppb in stream sediments and coinciding with a shift from Isopoda gathering/collector benthic feeders to Gastropoda scrapers/grazers classes. FT-ICR-MS findings showed that surface soils of agriculturally impacted sites contained high fractions of phenolic structures, where sediments from the drain were highly aliphatic and processed SOM. Together, we hypothesize that soluble polyphenols in surface soils may facilitate the transport of neonicotinoids to sediments in as little as three months as rainfall increases before the biological processing of decomposed SOM may release neonicotinoids to benthic macroinvertebrates. For the first time, our study proposes novel mechanisms of neonicotinoid pesticide transport in agricultural drains to help predict neonicotinoid transport and ecological consequences.