The increasing use of manufactured nanomaterials (MNMs) and their inevitable release into the environment, especially via wastewater treatment plants (WWTPs), poses a potential threat for aquatic organisms. The characterization of MNMs with analytical tools to comprehend their fate and effect on the ecosystem is hence of great importance for environmental risk assessment. We herein report, for the first time, the investigation of physicochemical transformation processes during artificial wastewater treatment of silver (Ag-NPs) and titanium dioxide nanoparticles (TiO2-NPs) via selected area electron diffraction (SAED). TiO2-NPs with an anatase/rutile ratio of ∼80/20 were found to not undergo any physicochemical transformation, as shown via previous energy-dispersive X-ray analysis (EDX) elemental mapping and crystal structure analysis via SAED. In contrast, Ag-NPs were colocalized with substantial amounts of sulfur (Ag/S ratio of 1.9), indicating the formation of Ag2S. SAED ultimately proved the complete transformation of face-centered cubic (fcc) Ag-NPs into monoclinic Ag2S-NPs. The size distribution of both nanomaterials remained virtually unchanged. Our investigations show that cloud point extraction of NPs and their subsequent crystal structure analysis via SAED is another valuable approach toward the comprehensive investigation of wastewater-borne MNMs. However, the extraction procedure needs optimization for environmentally low NP concentrations.