The contribution of the form of silver nanomaterials (nAg) towards toxicity in aquatic organisms is not well understood. The purpose of this study was to examine the toxicity of various structures (sphere, cube and prism) of nAg in Dreissena bugensis mussels. Mussels were exposed to increasing concentrations of polyvinyl-coated nAg of the same size for 96 h at 15 °C. They were then analyzed for biophysical changes in the cytoplasm (viscosity, protein aggregation and lipids), neuro-activity (fractal kinetics of acetylcholinesterase (AChE)), oxidative stress (labile zinc (Zn) and lipid peroxidation) and inflammation (arachidonate cyclooxygenase). Although some decreasing effects in protein aggregation were observed, viscosity was more strongly decreased in mussels exposed to spheric and prismatic nAg. The activity of AChE was significantly decreased in the following form-dependent manner: prismatic > cubic > spheric nAg. The fractal dimension of AChE reactions was reduced by all geometries of nAg, while dissolved Ag had no effects. For nanoparticles with the same coating and relative size, spheric nAg produced more significant changes towards the fractal dimension of AChE, while prismatic nAg increased both protein aggregation and viscosity, whereas cubic nAg decreased protein aggregation in the cytoplasm. It is concluded that the geometries of nanoparticles could influence toxicity in aquatic organisms.