The environmental transport and fate of nanoscale zero-valent iron particles (nZVI) in soil and groundwater can be altered by their hetero-aggregation with clay mineral particles (CMP). This study examines the interactions between bare or carboxymethyl cellulose (CMC)-coated nZVI with typical CMP, specifically kaolinite and montmorillonite. Methods include co-settling experiments, aggregation kinetic studies, electron microscopy, Derjaguin–Landau–Verwey–Overbeek (DLVO) and extended DLVO (EDLVO) energy analysis, and density functional theory calculations, focusing on the pH dependency of these interactions. The EDLVO theory effectively described the interactions between nZVI and CMP in aquatic environments. Under acidic conditions (pH 3.5), the interfacial interaction between bare nZVI and kaolinite is regulated by van der Waals forces, while complexation, van der Waals forces, and electrostatic attraction govern the interaction of bare nZVI with montmorillonite, primarily depositing on the SiO face. In contrast, the positively charged AlO face and edge of CMP are the main deposition sites for CMC-coated nZVI through hydrogen bonding, van der Waals forces, and electrostatic attraction. At neutral (pH 6.5) and alkaline (pH 9.5) conditions, both bare and CMC-coated nZVI predominantly attach to the AlO face and edge, facilitated by complexation or hydrogen bonding, alongside van der Waals forces. The attachment of CMC-coated nZVI to CMP surfaces shows reversible aggregation or deposition due to the steric repulsion from the CMC coating. These findings hold significant implications for the environmental applications and risk of nZVI.