The study evaluated removal efficiency of 43 pesticides from water by thin-film composite polyamide membrane indigenously prepared by interfacial polymerization of 1,3-phenylenediamine and 1,3,5 trimesoyl chloride coated on asymmetric polysulfone support. Membrane performance was evaluated by gas and liquid chromatography mass spectroscopy determination of multiple pesticides remaining in feed and permeated water following the application of pesticides each @ 0.02, 0.05, and 0.10 mg/L in de-ionized water. The membrane was most efficient in the rejection of persistent organochlorine insecticides, viz. endosulfans (100%), dichlorodiphenyltrichloroethane (95%), and hexachlorocyclohexane (92%). Out of 43 selected pesticides, 33 were removed by > 80%. Size exclusion mass transfer played a significant role for molecules to pass through the membrane as observed for endosulfan isomers, endosulfan sulphate, and difenoconazole with molecular weight > 400. Pesticide rejection was also related to hydrophobicity (Log P). Hydrophobic pesticides with log P > 4.5 were rejected by > 80%, while monocrotophos with less hydrophobicity (log P = − 0.22) exhibited poor rejection (38%). Water flux decreased with an increase in pesticide concentration. The process of pesticide filtration was optimized at 200 psi. The results indicated the potential of the membrane to remove pesticides from water.