Magnetic ion exchange resins (MIEX) were combined with nanofiltration (NF) in one single process to mitigate fouling by humic acids (HA). MIEX effectiveness in controlling NF fouling was investigated under different feed chemical conditions and employing two types of NF membranes (NF270, NF90). Fouling layer thickness was determined using novel helium ion microscopy, which allowed analysis of the membrane surface without sample alteration. Without MIEX, significant flux reduction (53-78%) due to irreversible organic fouling was observed for NF90, while fouling of NF270 was mostly reversible (15-23% irreversible flux reduction). This difference stems partially from the different ability of the two membranes to reject calcium, which affects the deposition of HA. Fouling was generally higher at alkaline pH due to calcite precipitation and formation of calcium-HA complexes. In the combined MIEX-NF process, fouling was reduced significantly. With NF90, irreversible flux reduction was half compared to the experiments run without resins, especially at neutral and alkaline pH (6-10). This was attributed to favorable HA-MIEX electrostatic interaction, which minimized the Ca-HA complexation and the availability of foulants for membrane deposition. Results demonstrated the effectiveness of MIEX to minimize fouling under different feed chemical conditions. This is of great importance considering the wide variability of real water chemistries in NF sources for drinking water production.