UV-initiated photomodification by a hydrophilic functional moiety (i.e., acrylic acid) was performed in and on a polypiperazineamide thin-film composite membrane. The sequence of the bilayers (i.e., acrylic acid and polypiperazineamide) was altered on a polysulfone membrane. The size exclusion order through the membranes was Atrazine > Simazine > 2,4,6-Trichlorophenol > 2,4-Dichlorophenol according to the molecular size, which was calculated by the quantum mechanical approach. Apart from the molecular size, the polarity and hydrophobicity of the molecules also influenced the separation. The performance of the membranes is based on size exclusion. The membrane with an inner layer of acrylic acid showed more blocking effect than the membrane with the same layer on the top of polypiperazineamide membrane and the unmodified polypiperazineamide membrane.