Polyamide (PA) membranes comprise most of the reverse osmosis membranes currently used for desalination and water purification. However, their fouling mechanisms with natural organic matter (NOM) is still not completely understood. In this work, we studied three different types of PA membranes: a laboratory made PA, a commercial PA, and a multiwalled carbon nanotube (CNT-PA nanocomposite membrane during cross-flow measurements by NaCl solutions including NOM, humic acid (HA), or alginate, respectively). Molecular dynamic simulations were also used to understand the fouling process of NOM down to its molecular scale. Low molecular weight humic acid binds to the surface cavities on the PA structures that leads to irreversible adsorption induced by the high surface roughness. In addition, the larger alginate molecules show a different mechanism, due to their larger size and their ability to change shape from the globule type to the uncoiled state. Specifically, alginate molecules either bind through Ca2+ bridges or they uncoil and spread on the surface. This work shows that carbon nanotubes can help to decrease roughness and polymer mobility on the surfaces of the membranes at the molecular scale, which represents a novel method to design antifouling membranes.