Nanofiltration (NF) process remains ineffective in removing neutral pollutants. The variable conditions of real water matrices further complicate the mechanisms of rejection. This study employed premixing and prefouling experiments to isolate the individual contributions of the fouling layer and solute-solute interactions to overall rejection. Our findings reveal that calcium ions (Ca2+) play a critical role by altering the properties of humic acid (HA) clusters. Specifically, Ca2+ minimizes HA cluster size at 0.2 mM, leading to a denser fouling layer and inducing the most significant concentration polarization. Furthermore, Ca2+ enhances the hydrophobicity of HA clusters, thereby suppressing hydrogen bonding with neutral pollutants. Overall, concentration polarization has a limited effect on the rejection of neutral pollutants. However, HA-pollutant binding plays a major role in removing small neutral molecules (e.g., erythritol and acetaminophen), which are hard to retain otherwise. Ca2+ disrupts these binding interactions and results in a notable decrease in rejection. Through validation with real water samples, this study identifies the intrinsic factors that cause the discrepancy in rejection performance between ultrapure water and complex aquatic environments. These insights provide a foundation for developing targeted water quality regulation strategies to improve the NF removal efficiency of neutral pollutants.