Emerging and fugitive contaminants (EFCs) released to our biosphere have caused a legacy- and continuing-threat to human and ecological health, contaminating air, water, and soil. Polluted media are closely linked to food security through plants, especially agricultural crops. However, measuring EFC's in plant tissues remains difficult, and high-throughput screening is of greater challenge. A novel rapid freeze-thaw/centrifugation extraction followed by high performance liquid chromatography - tandem mass spectrometry (HPLC-MS/MS) analysis was developed for high-throughput quantification of eleven EFCs with diverse chemical properties, including: estriol, codeine, oxazepam, 2,4-dinitrotoluene, 1,3,5-trinitroperhydro-1,3,5-triazine, bisphenol-A, triclosan, caffeine, carbamazepine, lincomycin, and DEET, in three representative crops, corn, tomato, and wheat. The internal aqueous solution, i.e. sap, is liberated via a freeze/thaw cycle, and separated from macromolecules utilizing molecular weight cut-off membrane centrifugal filtration. Detection limits ranged from 0.01 μg L-1 to 2.0 μg L-1. Recoveries of spiked analytes in three species ranged from 83.7% to 109%. Developed methods can rapidly screen EFCs in agriculture crops and can assess pollutant distribution at contaminated sites and gain insight on EFCs transport in plants to assess transmembrane migration in vascular organisms. The findings contribute significantly to environmental research, food security, and human health, as it assesses the first step of potential entry into the food chain, that being transmembrane migration and plant uptake, the primary barrier between polluted waters or soils and our food.