The presence of sub-micron-sized plastics in the environment has been increasing, with the possible risks of these particles remaining relatively unknown. In order to assess the toxicity of these particles, 100 nm diameter green fluorescent nano-polystyrene spheres (NPS) (20–60 mg/L) were exposed to zebra mussels (Dreissena polymorpha) to investigate the mortality, clearance rate and stress-related biomarker responses. D. polymorpha were collected and analysed with standard OECD toxicological tests and biomarker analysis to detect both physical and biochemical responses after exposure to NPS. The toxicity of the NPS to D. polymorpha was low, with 60 mg/L NPS causing a mortality rate of 11.1% at 96 h which was statistically significant compared to the 4.2% control. No statistical change could be found for the condition factor (kc) of D. polymorpha after NPS exposure. Clearance rates in D. polymorpha using R. subcapitata algae showed NPS-exposed mussels had a reduction of filtering efficiency of up to 30.5%. Bioassay testing shows a mixed but undeniably negative response from the D. polymorpha to the NPS, notably a significant rise in DNA Strand Breaks (DSB) and Metallothionein (MT) responses for high NPS concentrations. Additionally, Lipid Peroxidation (LPO) and Ferric Reducing Antioxidant Power (FRAP) assay tests showed a significant increase in response from the higher (>40 mg/L) concentrations of NPS exposure. Although Glutathione S-Transferase (GST) assay showed no statistical change from the control for all NPS-exposed samples, an increase of 20% had occurred for 60 mg/L NPS. Overall, a minimal toxic response from D. polymorpha to the NPS exposure below 40 mg/L was seen. After 40 mg/L NPS, mussels presented more acute toxicity in terms of mortality, along with reduced algal clearance rates and anincrease in biomarker response. This study revealed a clear induction of oxidative stress and DSB in the digestive gland of zebra mussels following exposure to nano-polystyrene. While these findings provide valuable insights into the potential harmful effects of nanoplastics in freshwater bivalves, further studies are necessary to help understand the level of threat plastic pollution may pose to the health of freshwater ecosystems.