To investigate the effect of pH on nanoparticle aggregation and transport in porous media, we quantified nanoparticle transport in two-dimensional structures. Titania was used as a model compound to explore the effects of surface potential on particle mobility in the subsurface. Results show that pH, and therefore, surface potential and aggregate size, dominate nanoparticle interactions with each other and surfaces. In each solution, nanoparticle aggregate size distributions were bimodal or trimodal, and aggregate sizes increased as the pH approached the pH of the point of zero charge (pHzpc). Over 80% of suspended particles and aggregates were mobile over the pH range of 1-12, except close to the pHzpc of the surfaces, where the particles are highly aggregated. The effect of pH on transport is not symmetric around the pHzpc of the particles due to charging of the channel surfaces. However, transport speed of nanoparticle aggregates did not vary with pH. The surface element integration technique, which takes into account the effect of curvature of particles on interaction energy, was used to evaluate the ability of theory to predict nanoparticle transport.