The increasingly widespread use of engineered nanoparticles in medical, industrial, and food applications has raised concerns regarding their potential toxicity to humans and the environment. Silicon dioxide nanoparticles (SiO₂ NPs), which have relatively low direct toxicity, have been increasingly applied in both consumer products and biomedical applications, leading to significantly higher exposure for humans and the environment. We carried out a toxicity assessment of SiO₂ NPs using the common water flea D. magna by focusing on physiological and behavioral indicators such as heart rate, swimming performance, and growth. Exposure to SiO₂ NPs did not produce acute or chronic toxicity at limited concentrations (<100 μg/mL), but did have statistically significant negative effects on heart rate, swimming distance, and body size. The use of fluorescein isothiocyanate in a silica matrix allowed the tracing and visualization of clear SiO₂ NP accumulation in D. magna, which was confirmed by ICP-MS. Although exposure to SiO₂ NPs seemed to affect cardiac and swimming performance, such end-point experiments may be insufficient to fully understand the toxicity of these nanoparticles. However, the physiological and behavioral changes shown here suggest potential adverse effects on the aquatic environment by substances previously considered nontoxic.