Considering the co-presence of body fluids and haloacetic acids (HAAs) in swimming pool waters (SPWs), as well as the potential for interaction among these substances and membranes, we have conducted a systematic investigation into the impact of body fluid analogue (BFA) on membrane performance. The minor impact of BFA on the rejection behavior of NF90 was attributed to its dominant effect of size exclusion. However, for NF270, 30 mg/L BFA increased water flux by 5%, decreased NaCl rejection from 59% to 47%, and decreased HAA rejection from 88% to 75%. The carboxyl-based components in BFA, including citric acid (CA) and hippuric acid (HA), were mainly responsible for the varied performance. Carboxyl-based components reduced the negative charge on membrane surfaces, increased the effective pore size and hydrophilicity, resulting in an increase for water flux and a decrease for NaCl and HAA rejection. The amine-based components (other BFA components with CA, HA, and salt excluded) did not directly influence the membrane performance, but their effect became remarkable under the coexistence of carboxyl-based components. The amine-based components neutralized the effect of the carboxyl-based components by forming hydrogen bonds. The practical application of membrane technology for water purification can be better predicted by the underlying mechanism for resolving the interaction among polyamide membranes, organic substances, and trace contaminants.