Red-light-emitting water-soluble semiconducting quantum dots (QDs) were synthesized by using a wide variety of commercially available thiol-type capping agents. QDs with a negatively charged nanosurface showed excellent selectivity for paraquat (PQ) at pH 7.4 over other commonly encountered pesticides/herbicides, including diquat (DQ). The presence of a 4,4'-bis-pyridinium unit in PQ enabled it to initiate long-range aggregation, thereby leading to the formation of nanostructures with excellent emission-quenching behavior. Precoated quartz plates were developed as a low-cost, portable sensor for the on-site detection of PQ in both natural water and human urine. Estimation of the PQ concentration was performed in different commercial formulations and the detection of PQ contamination in adulterated dairy product was also achieved with excellent sensitivity. Finally, we screened more than 50 different food items, including vegetables, fruits, cereals, and fodders, to construct a generalized marker for any residual PQ in such specimens.