Nanoplastics (NP) in the environment have become a growing concern in today’s society. The effects of the ingestion of NPs in organisms, aquatic in particular, is still relatively unknown. This study aims to examine NP internalization in different regions of the water flea (Daphnia magna) intestinal epithelium. Moreover, we tested varying sizes (0.5 μm and 1.0 μm mean diameter) of NP and compared their relative internalization.. We hypothesized that if D. magna are exposed to varying sizes of NP, then the gut will be able to internalize the smallest size in the highest concentration compared to the largest size in minimal concentration. The study’s findings showed that the hypothesis was not supported; instead, the largest NP (green) was found to be internalized more than the smallest NP (red). The study also revealed that internalization occurred more frequently in the midgut than the hindgut, a region of the intestine that is important for nutrient uptake. This study contributes to a foundation of understanding of the impacts of NP exposure on intestinal epithelium internalization, and possibly, other organ systems. Not only is this research relevant to aquatic organisms like D. magna, but organisms such as humans. Understanding the effects of NPs on the neurological and chemical aspects of the body could revolutionize the materials we use in everyday life and how medicine can be used within the body.