Widespread application of neonicotinoids has led to their proliferation in waters. Despite low neonicotinoid hydrophobicity, our prior studies implicated granular activated carbon (GAC) in neonicotinoid removal. Based on known receptor binding characteristics, we hypothesized that the insecticidal pharmacophore influences neonicotinoid sorption. Our objectives were to illuminate drivers of neonicotinoid sorption for parent neonicotinoids (imidacloprid, clothianidin, thiamethoxam, and thiacloprid) and pharmacophore-altered metabolites (desnitro-imidacloprid and imidacloprid urea) to GAC, powdered activated carbon, and carbon nanotubes (CNTs). Neonicotinoid sorption to GAC was extensive and largely irreversible, with significantly greater sorption of imidacloprid than desnitro-imidacloprid. Imidacloprid and imidacloprid urea (electronegative pharmacophores) sorbed most extensively to nonfunctionalized CNTs, whereas desnitro-imidacloprid (positive pharmacophore) sorbed most to COOH-CNTs, indicating the importance of charge interactions and/or hydrogen bonding between the pharmacophore and carbon surface. Water chemistry parameters (temperature, alkalinity, ionic strength, and humic acid) inhibited overall neonicotinoid sorption, suggesting that pharmacophore-driven sorption in real waters may be diminished. Analysis of a full-scale drinking water treatment plant GAC filter influent, effluent, and spent GAC attributes neonicotinoid/metabolite removal to GAC under real-world conditions for the first time. Our results demonstrate that the neonicotinoid pharmacophore not only confers insecticide selectivity but also impacts sorption behavior, leading to less effective removal of metabolites by GAC filters in water treatment.