The unique physicochemistry and potential toxicity of manufactured nanoparticles (NPs) requires innovative approaches for the assessment of toxicity to aquatic organisms. Here, the toxicity of Cu-NPs, Ag-NPs and TiO2-NPs on the lateral line system of free-swimming zebrafish embryos was investigated and compared to appropriate metal salts or bulk material controls. Fish were exposed for 4 h at 96-h post-fertilization. Metal salt (CuSO4 and AgNO3) controls reduced the number of functional lateral line neuromasts (LLN) to <5% of unexposed controls, but no effect on LLN was observed for TiO2-NPs or Ag-NPs. Exposure to Cu-NPs caused only a 15% reduction in LLN. Performance of positive rheotaxis was reduced by Cu-NPs, Ag-NPs, and the metal salt controls. The data show that some metal NPs can affect LLN and fish behaviour (rheotaxis) important for survival, and that effects were different from those of comparable metal ion controls. Capsule: We demonstrate that behaviour is a particularly sensitive indicator of metal NP exposure in fish and highlight the interaction between behaviour and external tissue surfaces.