The data here provided are the video recordings of nanoparticles of different sizes and charges in different media. Deionized water (as a control) and three differently viscous agar-hyaluronic acid hydrogels (used as vitreous humour in vitro models). The videos were recorded with a monochromatic camera (Axiocam305, Carl Zeiss) in an Axio Observer.Z1 m (Carl Zeiss, DE) inverted optical microscope.