The removal of five neonicotinoid insecticides, acetamiprid (ACE), chlothianidin (CLO), imidacloprid (IMI), thiacloprid (THC), and thiamethoxam (THM), was explored using various commercial ultrafiltration (UF) and nanofiltration (NF) membranes. Several modification techniques have also been implemented for one UF membrane, including immersion in hot water, sodium hydroxide, and ethanol solutions, as well as polymerization with monomers such as polyethyleneimine (PEI) and trimesoyl chloride (TMC), to improve micropollutant retention while maintaining adequate permeability. The results show that only immersion in ethanol (60% solution or absolute ethanol) was a suitable immersion technique for improving membrane performance. The use of various reagents and conditions for the membrane surface modification via polymerization yielded the best results, with the sequential application of PEI+TMC+60°C followed by immersion in glycerol solution (GLY) being the most efficient. Once the optimal modification procedure was established, these membranes were tested with real water matrices (two secondary effluents from wastewater treatment plants (WWTP) and a surface water sample) in which the neonicotinoids were dissolved. The modified UF membrane showed improved retention levels compared with commercial UF and NF membranes, demonstrating greater efficiency in retaining neonicotinoids under real water conditions. Therefore, the proposed modification process is a promising alternative to commercial membranes for removing micropollutants from urban wastewater.