Polymer coatings on nano-sized remediation agents and subsurface heterogeneity will affect their transport, likely in a pH-dependent manner. The effect of pH on the aggregation of polymer-coated nanoscale zerovalent iron (nZVI) and its deposition onto sand and clay (kaolinite) surfaces was studied. nZVI coatings included a high molecular weight (90 kg/mol) strong polyanion, poly(methacrylic acid)-b-(methy methacrylate)-b-(styrenesulfonate) (PMAA-PMMA-PSS) and a low molecular weight (2.5 kg/mol) weak polyanion, polyaspartate. Aggregation and deposition increased with decreasing pH for both polyelectrolytes. The extent was greater for the low MW polyaspartate coated nZVI. Enhanced deposition at lower pH was indicated because the elutability of polyaspartate-modified hematite (which did not aggregate) also decreased at lower pH. The greater deposition onto clay minerals compared to similar sized silica fines is attributed to charge heterogeneity on clay mineral surfaces, which is sensitive to pH. Heteroaggregation between kaolinite particles and nZVI over the pH range 6-8 confirmed this assertion. Excess unadsorbed polyelectrolyte in solution (100mg/L) enhanced the transport of modified nZVI by minimizing aggregation and deposition onto sand and clay. These results indicate that site physical and chemical heterogeneity must be considered when designing an nZVI emplacement strategy.