Information about the influence of surface charges on nanoplastics (NPLs) transport in porous media, the influence of NPL concentrations on porous media retention capacities, and changes in porous media adsorption capacities in the presence of natural water components are still scarce. In this study, laboratory column experiments are conducted to investigate the transport behavior of positively charged amidine polystyrene (PS) latex NPLs and negatively charged sulfate PS latex NPLs in quartz sand columns saturated with ultrapure water and Geneva Lake water, respectively. Results obtained for ultrapure water show that amidine PS latex NPLs have more affinity for negatively charged sand surfaces than sulfate PS latex NPLs because of the presence of attractive electrical forces. As for the Geneva Lake water, under natural conditions, both NPL types and sand are negatively charged. Therefore, the presence of repulsion forces reduces NPL’s affinity for sand surfaces. The calculated adsorption capacities of sand grains for the removal of both types of NPLs from both types of water are oscillating around 0.008 and 0.004 mg g−1 for NPL concentrations of 100 and 500 mg L−1, respectively. SEM micrography shows individual NPLs or aggregates attached to the sand and confirms the limited role of the adsorption process in NPL retention. The important NPL retention, especially in the case of negatively charged NPLs, in Geneva Lake water-saturated columns is related to heteroaggregate formation and their further straining inside narrow pores. The presence of DOM and metal cations is then crucial to trigger the aggregation process and NPL retention.